Haplotypes Associated with Improved Stacked Trait Performance in Transgenic Plants

ABSTRACT

The present invention provides methods and compositions for the identification and selection of loci modulating phenotypic expression of an herbicide tolerance trait in plant breeding. In addition, methods are provided for screening germplasm entries for the performance and expression of this trait.

CROSS-REFERENCE TO RELATED APPLICATIONS

This International Patent Application claims the benefit of U.S. PatentApplication No. 61/779,739, filed Mar. 13, 2013; U.S. Patent ApplicationNo. 61/753,725, filed Jan. 17, 2013; U.S. Patent Application No.61/753,693, filed Jan. 17, 2013; U.S. Patent Application No. 61/650,869,filed May 23, 2012; and U.S. Patent Application No. 61/650,852, filedMay 23, 2012, each of which is incorporated herein by reference in itsentirety.

INCORPORATION OF SEQUENCE LISTING

A sequence listing containing the file named“46_(—)21_(—)59246_A_PCT.txt” which is 33,292 bytes (measured inMS-Windows) and created on May 20, 2013, comprises 56 nucleotidesequences, is provided herewith via the USPTO's EFS system and is hereinincorporated by reference in its entirety.

INCORPORATION OF TABLE 2

A listing of various soybean linkage group L (chromosome 19) markers isprovided herewith in the Specification as Table 2.

BACKGROUND

International Patent Application Publication WO 2012/031097 describesgenetic regions of soybean linkage group L that contain polymorphic locithat are associated with an undesirable “yellow flash” phenotype that isobserved in the foliage of certain soybean varieties that comprise atransgene that confers resistance to glyphosate that are exposed toglyphosate.

SUMMARY

“Dicamba intolerance” is an undesirable phenotype observed in certainsoybean varieties that comprise a transgene that can confer resistanceto the broad-spectrum herbicide dicamba. After application of dicamba,it has been discovered that the leaves of certain soybean plantvarieties comprising the transgene that confers resistance to dicambacan exhibit a “dicamba intolerance phenotype” comprising malformation(epinasty) of the main stem and petioles upon exposure to dicamba. Theepinastic growth habit of such “dicamba intolerant” transgenic plants ismanifest in pronounced bending/twisting of the main stem and petioles.In dicamba intolerant transgenic soybean plants exposed to dicamba, theupper nodes and petioles may die, but lower portion of the plant mayremain vegetative and new growth can be limited. However, other soybeanplant varieties containing the same transgene that confers resistance todicamba do not exhibit the dicamba intolerance phenotype when co-exposedto the same dosage of dicamba. The dicamba intolerance phenotype can beobserved within approximately 2 to 10 days after herbicide applicationin certain soybean varieties comprising the transgene that confersresistance to dicamba. The dicamba intolerance phenotype is undesirableas it can lead to reduced yield in certain transgenic soybean plantvarieties exposed to dicamba.

Although the dicamba intolerance phenotype can be observed withinapproximately 2 to 10 days after dicamba application in certain soybeanvarieties comprising the transgene that confers dicamba resistance,distinct soybean varieties that comprise the same dicamba resistancetransgene integrated at the same chromosomal locus (i.e. the sametransgenic event) can show various degrees of dicamba intolerance uponexposure to high doses of dicamba. Some varieties comprising the dicambaresistance transgene insertion are highly tolerant to high dosages ofdicamba, showing no dicamba intolerance phenotype (i.e. a “dicambatolerance phenotype”), while other varieties comprising the same dicambaresistance transgene insertion are highly susceptible to high dosages ofdicamba, showing a severe dicamba intolerance phenotype. Provided hereinare soybean plants comprising an introgressed genomic region associatedwith a dicamba tolerance phenotype. Also provided herein are markersthat reside outside of a genomic region associated with a dicambatolerance phenotype and that facilitate breeding activities thatinclude, but are not limited to, introgression of this genomic region.Markers and specific alleles thereof that are associated with a dicambatolerance phenotype are also provided. Methods of obtaining a soybeanplant that exhibits a dicamba tolerance phenotype and methods ofobtaining a soybean plant comprising in its genome at least one dicambatolerance locus are also provided. Methods that provide for theintrogression of a genomic region associated with a dicamba tolerancephenotype into soybean germplasm that has a genomic region associatedwith a dicamba intolerance phenotype are also provided. Identificationof molecular markers associated with loci that confer the dicambatolerance phenotype has significant economic value. By using markersassociated with the dicamba tolerance trait, breeders can select soybeanvarieties with the favorable alleles (i.e. alleles that are notassociated with the dicamba intolerance trait) for use in traitintegration. They can also use the markers to help them eliminateunfavorable alleles (i.e. alleles that are associated with the dicambaintolerance trait) in soybeans. In certain embodiments, commerciallydesirable transgenic soybean lines that carry a genomic region that isassociated with a “dicamba tolerance” phenotype and tolerate highdosages of dicamba are thus provided.

It has also been surprisingly observed that soybean plants comprisingthe dicamba tolerance loci, a transgene conferring resistance todicamba, and a transgene conferring resistance to glyphosate alsoexhibit improved reproductive tolerance to glyphosate applicationrelative to plants with the same two transgenes that lack the dicambatolerance loci. Although the glyphosate reproductive intolerancephenotype can be observed after late stage (i.e. V6/R1) glyphosateapplication in certain soybean varieties comprising the transgenes thatconfer dicamba and glyphosate resistance, distinct soybean varietiesthat comprise the same dicamba and glyphosate resistance transgeneintegrated at the same chromosomal loci (i.e. the same transgenicevents) can show various degrees of glyphosate reproductive intolerance(i.e. varying degrees of sterility) upon such exposure to glyphosate.Some varieties comprising the dicamba and glyphosate resistancetransgene insertions are highly tolerant to late stage glyphosateapplication, showing no sterility phenotype (i.e. a “glyphosatereproductive intolerance phenotype”), while other varieties comprisingthe same dicamba and glyphosate resistance transgene insertions arehighly susceptible to late stage glyphosate application, showing varyinglevels of sterility. Provided herein are soybean plants comprising anintrogressed genomic region associated with a dicamba tolerancephenotype that also provide for reproductive tolerance to glyphosate.Also provided herein are markers that reside outside of a genomic regionassociated with a dicamba tolerance/reproductive tolerance to glyphosatephenotype and that facilitate breeding activities that include, but arenot limited to, introgression of this genomic region. Markers andspecific alleles thereof that are associated with a dicambatolerance/reproductive tolerance to glyphosate are also provided.Methods of obtaining a soybean plant that exhibits reproductivetolerance to glyphosate and methods of obtaining a soybean plantcomprising in its genome at least one dicamba tolerance/reproductivetolerance to glyphosate locus are also provided. Methods that providefor the introgression of a genomic region associated with reproductivetolerance to glyphosate into soybean germplasm that has a genomic regionassociated with a reproductive tolerance to glyphosate are alsoprovided. Identification of molecular markers associated with loci thatconfer reproductive tolerance to glyphosate has significant economicvalue. By using markers associated with the reproductive tolerance toglyphosate trait, breeders can select soybean varieties with thefavorable alleles (i.e. alleles that are not associated with theglyphosate reproductive intolerance trait) for use in trait integration.They can also use the markers to help them eliminate unfavorable alleles(i.e. alleles that are associated with the glyphosate reproductiveintolerance trait) in soybeans. In certain embodiments, commerciallydesirable transgenic soybean lines that carry a genomic region that isassociated with a “glyphosate reproductive tolerance” phenotype andtolerate late stage (i.e. V6/R1) application of glyphosate are thusprovided.

Methods of identifying a soybean plant that comprises a genotypeassociated with a dicamba tolerance phenotype and/or a glyphosatereproductive tolerance phenotype are thus provided.

In certain embodiments, the plurality of soybean plants comprises apopulation that is obtained by: i) crossing a parent plant comprising atleast one dicamba tolerance locus with a parent plant comprising atleast one dicamba intolerance locus; or, ii) obtaining seed or progenyfrom a parental plant segregating for at least one dicamba tolerancelocus. In certain embodiments, the population contains plants thatcomprise a transgene that confers resistance to dicamba. In certainembodiments, the aforementioned methods can further comprise the step ofassaying for the presence of at least one additional marker, where theadditional marker is either linked or unlinked to the linkage group Lgenomic region. In certain embodiments of the aforementioned methods,the plurality of soybean plants, the soybean plant, and/or progenythereof are exposed to a dosage of dicamba sufficient to cause dicambaintolerance in a susceptible variety. In certain embodiments of theaforementioned methods, a plant that exhibits a dicamba tolerancephenotype is selected.

Also provided herewith are methods for producing a soybean plantcomprising in its genome at least one introgressed dicamba tolerancelocus. Also provided herewith are soybean plants comprising anintrogressed dicamba tolerance locus made by the aforementioned methods.In certain embodiments, a soybean plant comprising an introgresseddicamba tolerance locus and one or more polymorphic loci comprisingalleles or combinations of alleles that are not found in a dicambatolerant soybean variety and that are linked to the introgressed dicambatolerance locus, where the plant is produced by the aforementionedmethods are provided.

Also provided are soybean plants comprising an introgressed dicambatolerance locus and one or more polymorphic loci comprising alleles orcombinations of alleles that are not found in a dicamba tolerant soybeanvariety and that are linked to the introgressed dicamba tolerance locus.

Methods of identifying a soybean plant that comprises a genotypeassociated with dicamba tolerance and/or reproductive tolerance toglyphosate are thus provided. In certain embodiments, the methods cancomprise detecting in a soybean plant an allele in at least one geneticlocus associated with dicamba tolerance and/or reproductive tolerance toglyphosate, where the genetic locus is in a linkage group L genomicregion flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO:12), and denoting that the plant comprises a genotype associated withdicamba tolerance. In certain embodiments, the methods can furthercomprise the step of selecting the denoted plant from a population ofplants. In certain embodiments, the plant comprises a transgene thatconfers resistance to dicamba and/or a transgene that confers resistanceto glyphosate. In certain embodiments, the soybean plant or progenythereof is exposed to a dosage of dicamba sufficient to cause adeleterious effect in a susceptible variety comprising the transgeneand/or is exposed to a dosage of glyphosate sufficient to causesterility in a susceptible variety comprising the transgene(s). Incertain embodiments of any of the aforementioned methods, a plant thatexhibits dicamba tolerance and/or reproductive tolerance to glyphosateis selected. In certain embodiments of any of the aforementionedmethods, a genotype associated with a dicamba tolerance comprises atleast one polymorphic allele of at least one marker in a firstsub-region of the linkage group L region that is flanked by lociM0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least onepolymorphic allele of at least one marker in a second sub-region of thelinkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9)and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele ofat least one marker in a third sub-region of the linkage group L regionthat is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8)is provided. In certain embodiments of any of the aforementionedmethods, the genotype associated with dicamba tolerance comprises atleast one polymorphic allele of at least one marker in the linkage groupL region selected from the group consisting of a TT allele M0205350 (SEQID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele ofM0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ IDNO:52).

Methods for obtaining a soybean plant comprising in its genome at leastone dicamba tolerance locus are also provided. In certain embodiments,these methods can compromise the steps of: (a) genotyping a plurality ofsoybean plants with respect to at least one genetic locus in a linkagegroup L genomic region flanked by loci M0205928 (SEQ ID NO: 4) andBU765955 (SEQ ID NO: 12); and, (b) selecting a soybean plant comprisingin its genome at least one genetic locus comprising a genotypeassociated with dicamba tolerance. In certain embodiments of thesemethods, the genotype associated with dicamba tolerance comprises atleast one polymorphic allele of at least one marker in a firstsub-region of the linkage group L region flanked by loci M0205928 (SEQID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least one polymorphicallele of at least one marker in a second sub-region of the linkagegroup L region that is flanked by loci BU551363 (SEQ ID NO: 9) andBU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele of atleast one marker in a third sub-region of the linkage group L regionthat is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ IDNO:8). In certain embodiments of any of these aforementioned methods,the genotype associated with dicamba tolerance comprises at least onepolymorphic allele of at least one marker in the first linkage group Lregion, the first sub-region, the second sub-region, or the thirdsub-region, where the marker is selected from the group consisting of aTT allele M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO:5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele ofNGMAX008197032 (SEQ ID NO:52). In certain embodiments of these methods,the plurality of soybean plants comprises a population that is obtainedby: i) crossing a parent plant comprising at least one dicamba tolerancelocus with a parent plant comprising at least one dicamba sensitivitylocus; or, ii) obtaining seed or progeny from a parental plantsegregating for at least one dicamba tolerance locus. In certainembodiments of these methods, the population contains plants thatcomprise at least one transgene that confers resistance to dicambaand/or a transgene that confers resistance to glyphosate. In certainembodiments of any of the aforementioned methods, the methods canfurther comprise the step of assaying for the presence of at least oneadditional marker, where the additional marker is either linked orunlinked to the linkage group L genomic region. In certain embodimentsof any of the aforementioned methods, the plurality of soybean plants,the soybean plant, and/or progeny thereof are exposed to a dosage ofdicamba sufficient to cause a deleterious effect in a susceptiblevariety comprising the transgene and/or is exposed to a dosage ofglyphosate sufficient to cause sterility in a susceptible varietycomprising the transgene. In certain embodiments of any of theaforementioned methods, a plant that exhibits dicamba tolerance and/orreproductive tolerance to glyphosate is selected.

Methods for producing a soybean plant comprising in its genome at leastone introgressed dicamba tolerance locus are also provided. In certainembodiments, these methods comprise the steps of: (a) crossing a firstsoybean plant with a dicamba tolerance locus with a second soybean plantcomprising: a dicamba sensitivity locus in a first linkage group Lgenomic region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQID NO: 6) and/or at least one polymorphic allele of at least one markerin a second sub-region of the linkage group L region that is flanked byloci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or atleast one polymorphic allele of at least one marker in a thirdsub-region of the linkage group L region that is flanked by loci BU55345(SEQ ID NO:7) and M0114388 (SEQ ID NO:8) and at least one linkedpolymorphic locus not present in the first soybean plant to obtain apopulation segregating for the dicamba tolerance loci and the linkedpolymorphic locus; (b) detecting at least two polymorphic nucleic acidsin at least one soybean plant from the population, where at least one ofthe polymorphic nucleic acids is located in the first linkage group Lregion and/or the second linkage group L region and where at least oneof the polymorphic amino acids is a linked polymorphic locus not presentin the first soybean plant; and (c) selecting a soybean plant comprisinga genotype associated with dicamba tolerance and at least one linkedmarker found in the second soybean plant comprising a dicambasensitivity locus but not in the first soybean plant, thereby obtaininga soybean plant comprising in its genome at least one introgresseddicamba tolerance locus. In certain embodiments of these methods, atleast one of the first or the second soybean plants comprises atransgene that confers resistance to dicamba and/or a transgene thatconfers resistance to glyphosate. In certain embodiments of thesemethods, the population, the selected soybean plant, and/or progeny ofselected soybean plant is exposed to a dosage of dicamba sufficient tocause a deleterious effect in a susceptible variety comprising thetransgene and/or is exposed to a dosage of glyphosate sufficient tocause sterility in a susceptible variety comprising the transgene. Incertain embodiments of these methods, the polymorphic nucleic aciddetected in step (b) is detected with at least one marker selected fromthe group consisting of M0205350 (SEQ ID NO: 10), M0101742 (SEQ ID NO:5), M0102027 (SEQ ID NO: 11), and NGMAX008197032 (SEQ ID NO:52). Incertain embodiments of these methods, the polymorphic nucleic aciddetected in step (b) comprises a TT allele of M0205350 (SEQ ID NO: 10),a TT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ IDNO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certainembodiments of these methods, the polymorphic nucleic acid detected instep (b) is detected with marker M0205350 (SEQ ID NO: 10) or M0102027(SEQ ID NO: 11). In certain embodiments of these methods, thepolymorphic nucleic acids are detected with marker M0101742 (SEQ ID NO:5). In certain embodiments of these methods, the polymorphic nucleicacids are detected with marker NGMAX008197032 (SEQ ID NO:52). In certainembodiments of any of the aforementioned methods, the linked polymorphiclocus is detected with a genotypic marker, a phenotypic marker, or both.In certain embodiments of these methods, the linked polymorphic locus isdetected with a marker that is located within about 1000, 500, 100, 40,20, 10, or 5 kilobases (Kb) of the dicamba tolerance locus. In certainembodiments of these methods, the linked polymorphic locus is detectedwith at least one marker selected from the group consisting ofasmbl_(—)11856 (SEQ ID NO: 1), TC122822 (SEQ ID NO: 2), BI967232 (SEQ IDNO: 3), M0205537 (SEQ ID NO: 15), M0202715 (SEQ ID NO: 16), M0206286(SEQ ID NO: 17), M0206054 (SEQ ID NO: 18), and M0205375 (SEQ ID NO: 19).

Transgenic soybean plants comprising introgressed linkage group Lregions comprising at least one polymorphic allele of at least onemarker in a first sub-region of the linkage group L region that flankedby loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or atleast one polymorphic allele of at least one marker in a secondsub-region of the linkage group L region that is flanked by lociBU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least onepolymorphic allele of at least one marker in a third sub-region of thelinkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) andM0114388 (SEQ ID NO:8), where the polymorphic alleles are associatedwith dicamba tolerance and/or reproductive tolerance to glyphosate, andwhere the plant comprises a transgene that confers resistance to dicambaare also provided. In certain embodiments, the polymorphic allelescomprise a TT allele of M0205350 (SEQ ID NO: 10), a TT allele ofM0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and anAA allele of NGMAX008197032 (SEQ ID NO:52). In certain embodiments, thetransgenic plant exhibits dicamba tolerance. In certain embodiments, thetransgenic plant further comprises a transgene that confers resistanceto glyphosate and exhibits reproductive tolerance to glyphosate. Incertain embodiments of any one of the aforementioned methods, the plantfurther comprises at least one of a 2,4-D, glufosinate, bromoxynil,acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase),hydroxyphenyl pyruvate dioxygenase (HPPD), or sulfonylurea herbicideresistance transgenes and/or at least one transgene selected from thegroup of transgenes conferring insect resistance, nematode resistance,fungal resistance, an improvement in seed oil quantity, an improvementin seed oil quality, abiotic stress resistance, and intrinsic yieldincreases. In certain embodiments, the insect resistance conferringtransgene is a transgene that expresses an insecticidal Bacillusthuringiensis protein.

Also provided herein are soybean plants comprising a dicamba tolerancelocus, a transgene conferring resistance to glyphosate, a transgeneconferring resistance to dicamba, where the plants exhibit both improveddicamba tolerance and improved reproductive tolerance to glyphosaterelative to soybean plants comprising the same two transgenes butlacking the dicamba tolerance locus. Such improved reproductivetolerance to glyphosate is reflected in reduced sterility when theplants are exposed to glyphosate.

In certain embodiments, the dicamba tolerance locus provided herein canprovide for improved performance of additional combinations oftransgenic traits (i.e. “stacked transgenic traits”) in soybean plants.In such embodiments, the dicamba tolerance locus provided herein can bealternatively referred to and considered a “stacked transgenic traitimprovement” locus. Allele(s) of the dicamba tolerance locus or “stackedtransgenic trait improvement” locus that do not confer such dicambatolerance or such stacked transgenic trait improvements are referred toherein as dicamba sensitivity or “stacked transgenic trait sensitivity”loci. Transgenic plants comprising the stacked transgenic traitimprovement locus provided herein exhibit improved performance of bothtransgenes present in the transgenic plant relative to plants comprisingthe same two transgenes that lack the stacked transgenic traitimprovement locus. Such improved performance can manifest in any ofenhanced transgenic trait performance, increased transgene efficacy,and/or increased transgene expression. Transgenic plants comprising thestacked trait improvement locus and two transgenes are thus providedherein. Thus, in certain embodiments the two independent and distincttransgenes that exhibit improved performance in the presence of thestacked transgenic trait improvement locus both contribute to the sametrait. In certain embodiments, this same trait is selected from thegroup consisting of resistance to a single herbicide, resistance to aninsect, resistance to a nematode, resistance to a fungal disease,resistance to an abiotic stress, an improvement in seed oil quantity, animprovement in seed oil quality, and intrinsic yield increases. Incertain embodiments, the two transgenes can contribute to the sameherbicide resistance trait where the herbicide resistance is selectedfrom the group consisting of glyphosate, dicamba, 2,4-D, glufosinate,bromoxynil, synthetic auxins, and inhibitors of acetolactate synthase(ALS), acetyl CoA carboxylase (ACCase) and hydroxyphenyl pyruvatedioxygenase (HPPD) resistance. In certain embodiments, the twotransgenes can contribute to the same insect, fungal, or nematoderesistance trait where the resistance to the same insect, fungal, ornematode pest is by a different mode of action to provide for improvedpest resistance management. In other embodiments, the two transgenes canbe two independent and distinct transgenes that encode different genesbut contribute to a different trait. In certain embodiments, thisdifferent trait is independently selected from the group consisting ofresistance to one or more herbicide(s), resistance to one or moreinsect(s), resistance to one or more nematode(s), resistance to one ormore fungal disease(s), resistance to one or more abiotic stress(es),one or more improvement(s) in seed oil quantity or quantities, one ormore improvement(s) in seed oil quality or qualities, intrinsic yieldincreases, and combinations thereof. In certain embodiments the stackedtrait improvement locus is an herbicide tolerance locus that providesfor improved tolerance to at least two distinct herbicides in plantscomprising at least two transgenes that respectively confer resistanceto those two herbicides. In certain embodiments, the herbicide tolerancelocus provides for improved tolerance to at least two herbicidesselected from the group consisting of glyphosate, dicamba, 2,4-D,glufosinate, bromoxynil, synthetic auxins, and inhibitors ofacetolactate synthase (ALS), acetyl CoA carboxylase (ACCase) andhydroxyphenyl pyruvate dioxygenase (HPPD) resistance in plantscomprising at least two transgenes that confer resistance to those twoherbicides. In certain embodiments, the herbicide tolerance locusconfers improved tolerance to dicamba, improved reproductive toleranceto glyphosate, and improved tolerance to a synthetic auxin thatincludes, but is not limited to 2,4-D, in a plant comprising transgenesthat confer resistance to dicamba, glyphosate, and the synthetic auxinthat includes, but is not limited to 2,4-D. In certain embodiments, thetwo transgenes can confer a distinct herbicide resistance trait wherethe herbicide resistance is selected from the group consisting ofglyphosate, dicamba, 2,4-D, glufosinate, bromoxynil, synthetic auxinsother than 2,4-D, acetolactate synthase (ALS), acetyl CoA carboxylase(ACCase) and hydroxyphenyl pyruvate dioxygenase (HPPD) resistance.Provided herein are soybean plants comprising any combination of astacked trait improvement locus and at least two transgenes conferringherbicide tolerance selected from the group consisting of glyphosate,dicamba, 2,4-D, glufosinate, bromoxynil, synthetic auxins, andinhibitors of acetolactate synthase (ALS), acetyl CoA carboxylase(ACCase) and hydroxyphenyl pyruvate dioxygenase (HPPD). In certainembodiments, soybean plants comprising an introgressed stacked traitimprovement locus, at least one transgene selected from the groupconsisting of glyphosate, dicamba, 2,4-D, glufosinate, bromoxynil,synthetic auxins other than 2,4-D, acetolactate synthase (ALS), acetylCoA carboxylase (ACCase), hydroxyphenyl pyruvate dioxygenase (HPPD), andsulfonylurea herbicide resistance transgenes, and at least one transgeneselected from the group of transgenes conferring insect resistance,nematode resistance, fungal resistance, an improvement in seed oilquantity, an improvement in seed oil quality, abiotic stress resistance,and intrinsic yield increases are provided. In still other embodiments,soybean plants comprising an introgressed stacked trait improvementlocus, at least one transgene selected from the group consisting ofglyphosate, dicamba, 2,4-D, and at least one transgene conferringresistance to an insect are provided. In still other embodiments,soybean plants comprising an introgressed stacked trait improvementlocus, at least one transgene selected from the group consisting ofglyphosate, dicamba, glufosinate, and 2,4-D resistance conferringtransgenes, and at least one transgene conferring resistance to aninsect that encodes a Bacillus thuringiensis toxin are provided. Incertain embodiments, soybean plants comprising an introgressed stackedtrait improvement locus, a glyphosate and a dicamba resistanceconferring transgene, and a cry1Ac insect resistance transgene areprovided. In still other embodiments, soybean plants comprising at leastone herbicide resistance transgene selected from the group consisting ofa dicamba resistance conferring transgene. a glyphosate resistanceconferring transgene, a 2,4-D resistance conferring transgene, and aglufosinate resistance conferring transgene and/or at least onetransgene encoding a product that confers insect resistance selectedfrom the group consisting of a dsRNA that inhibits a target gene of aninsect pest, a patatin, a Bacillus thuringiensis insecticidal protein, aXenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, aBacillus laterosporous insecticidal protein, a Bacillus sphaericusinsecticidal protein, and a lignin are provided.

Methods of identifying a soybean plant that comprises a genotypeassociated with stacked transgenic trait improvement are thus provided.In certain embodiments, the methods can comprise detecting in a soybeanplant an allele in at least one genetic locus associated with stackedtransgenic trait improvement, where the genetic locus is in a linkagegroup L genomic region flanked by loci M0205928 (SEQ ID NO: 4) andBU765955 (SEQ ID NO: 12), and denoting that the plant comprises agenotype associated with stacked transgenic trait improvement. Incertain embodiments, the methods can further comprise the step ofselecting the denoted plant from a population of plants. In certainembodiments, the plant comprises at least two transgenes that contributeto the same trait. In certain embodiments, this same trait is selectedfrom the group consisting of resistance to a single herbicide,resistance to an insect, resistance to a nematode, resistance to afungal disease, resistance to an abiotic stress, an improvement in seedoil quantity, an improvement in seed oil quality, and intrinsic yieldincreases. In certain embodiments, the plant comprises at least twotransgenes that contribute to different traits. In certain embodiments,this different trait is independently selected from the group consistingof resistance to one or more herbicide(s), resistance to one or moreinsect(s), resistance to one or more nematode(s), resistance to one ormore fungal disease(s), resistance to one or more abiotic stress(es),one or more improvement(s) in seed oil quantity or quantities, one ormore improvement(s) in seed oil quality or qualities, intrinsic yieldincreases, and combinations thereof. In certain embodiments, the soybeanplant or progeny thereof is exposed to a dosage of an herbicidesufficient to cause a deleterious effect in a susceptible varietycomprising the transgene conferring resistance to that herbicide butlacking the stacked transgenic trait improvement locus. In certainembodiments of any of the aforementioned methods, a plant that exhibitsstacked transgenic trait improvement is selected. In certain embodimentsof any of the aforementioned methods, a genotype associated with stackedtransgenic trait improvement comprises at least one polymorphic alleleof at least one marker in a first sub-region of the linkage group Lregion that is flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQID NO: 6) and/or at least one polymorphic allele of at least one markerin a second sub-region of the linkage group L region that is flanked byloci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or atleast one polymorphic allele of at least one marker in a thirdsub-region of the linkage group L region that is flanked by loci BU55345(SEQ ID NO:7) and M0114388 (SEQ ID NO:8) is provided. In certainembodiments of any of the aforementioned methods, the genotypeassociated with stacked transgenic trait improvement comprises at leastone polymorphic allele of at least one marker in the linkage group Lregion selected from the group consisting of a TT allele M0205350 (SEQID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele ofM0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ IDNO:52).

Methods for obtaining a soybean plant comprising in its genome at leastone stacked transgenic trait improvement locus are also provided. Incertain embodiments, these methods can compromise the steps of: (a)genotyping a plurality of soybean plants with respect to at least onegenetic locus in a linkage group L genomic region flanked by lociM0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12); and, (b) selectinga soybean plant comprising in its genome at least one genetic locuscomprising a genotype associated with stacked transgenic traitimprovement. In certain embodiments, the plant comprises at least twotransgenes that contribute to the same trait. In certain embodiments,this same trait is selected from the group consisting of resistance to asingle herbicide, resistance to an insect, resistance to a nematode,resistance to a fungal disease, resistance to an abiotic stress, animprovement in seed oil quantity, an improvement in seed oil quality,and intrinsic yield increases. In certain embodiments, the plantcomprises at least two transgenes that contribute to different traits.In certain embodiments, this different trait is independently selectedfrom the group consisting of resistance to one or more herbicide(s),resistance to one or more insect(s), resistance to one or morenematode(s), resistance to one or more fungal disease(s), resistance toone or more abiotic stress(es), one or more improvement(s) in seed oilquantity or quantities, one or more improvement(s) in seed oil qualityor qualities, intrinsic yield increases, and combinations thereof. Incertain embodiments of these methods, the genotype associated withstacked transgenic trait improvement comprises at least one polymorphicallele of at least one marker in a first sub-region of the linkage groupL region flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ IDNO: 6) and/or at least one polymorphic allele of at least one marker ina second sub-region of the linkage group L region that is flanked byloci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or atleast one polymorphic allele of at least one marker in a thirdsub-region of the linkage group L region that is flanked by loci BU55345(SEQ ID NO:7) and M0114388 (SEQ ID NO:8). In certain embodiments of anyof these aforementioned methods, the genotype associated with stackedtransgenic trait improvement comprises at least one polymorphic alleleof at least one marker in the first linkage group L region, the firstsub-region, the second sub-region, the third sub-region, where themarker is selected from the group consisting of a TT allele M0205350(SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele ofM0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ IDNO:52). In certain embodiments of these methods, the plurality ofsoybean plants comprises a population that is obtained by: i) crossing aparent plant comprising at least one stacked transgenic traitimprovement locus with a parent plant lacking a stacked transgenic traitimprovement locus; or, ii) obtaining seed or progeny from a parentalplant segregating for at least one stacked transgenic trait improvementlocus. In certain embodiments of any of the aforementioned methods, themethods can further comprise the step of assaying for the presence of atleast one additional marker, where the additional marker is eitherlinked or unlinked to the linkage group L genomic region. In certainembodiments of any of the aforementioned methods, the plurality ofsoybean plants, the soybean plant, and/or progeny thereof are exposed toa dosage of an herbicide sufficient to cause a deleterious effect in asusceptible variety comprising the transgene conferring resistance tothat herbicide but lacking the stacked transgenic trait improvementlocus. In certain embodiments of any of the aforementioned methods, aplant that exhibits stacked transgenic trait improvement is selected.

Methods for producing a soybean plant comprising in its genome at leastone introgressed stacked transgenic trait improvement locus are alsoprovided. In certain embodiments, these methods comprise the steps of(a) crossing a first soybean plant with a stacked transgenic traitimprovement locus with a second soybean plant lacking a stackedtransgenic trait improvement locus in a first linkage group L genomicregion flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO:6) and/or at least one polymorphic allele of at least one marker in asecond sub-region of the linkage group L region that is flanked by lociBU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least onepolymorphic allele of at least one marker in a third sub-region of thelinkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) andM0114388 (SEQ ID NO:8) and at least one linked polymorphic locus notpresent in the first soybean plant to obtain a population segregatingfor the stacked transgenic trait improvement loci and the linkedpolymorphic locus; (b) detecting at least two polymorphic nucleic acidsin at least one soybean plant from the population, where at least one ofthe polymorphic nucleic acids is located in the first linkage group Lregion and/or the second linkage group L region and where at least oneof the polymorphic amino acids is a linked polymorphic locus not presentin the first soybean plant; and (c) selecting a soybean plant comprisinga genotype associated with stacked transgenic trait improvement and atleast one linked marker found in the second soybean plant lacking thestacked transgenic trait improvement locus but not found in the firstsoybean plant, thereby obtaining a soybean plant comprising in itsgenome at least one introgressed stacked transgenic trait improvementlocus. In certain embodiments, the first and/or second plant comprisesat least two transgenes that contribute to the same trait. In certainembodiments, this same trait is selected from the group consisting ofresistance to a single herbicide, resistance to an insect, resistance toa nematode, resistance to a fungal disease, resistance to an abioticstress, an improvement in seed oil quantity, an improvement in seed oilquality, and intrinsic yield increases. In certain embodiments, theplant comprises at least two transgenes that contribute to differenttraits. In certain embodiments, this different trait is independentlyselected from the group consisting of resistance to one or moreherbicide(s), resistance to one or more insect(s), resistance to one ormore nematode(s), resistance to one or more fungal disease(s),resistance to one or more abiotic stress(es), one or more improvement(s)in seed oil quantity or quantities, one or more improvement(s) in seedoil quality or qualities, intrinsic yield increases, and combinationsthereof. In certain embodiments of these methods, the population, theselected soybean plant, and/or progeny of selected soybean plant isexposed to a dosage of an herbicide sufficient to cause a deleteriouseffect in a susceptible variety comprising the transgene that confersresistance to the herbicide but lacking the stacked transgenic traitimprovement locus. In certain embodiments of these methods, thepolymorphic nucleic acid detected in step (b) is detected with at leastone marker selected from the group consisting of M0205350 (SEQ ID NO:10), M0101742 (SEQ ID NO: 5), M0102027 (SEQ ID NO: 11), and an AA alleleof NGMAX008197032 (SEQ ID NO:52). In certain embodiments of thesemethods, the polymorphic nucleic acid detected in step (b) comprises aTT allele of M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ IDNO: 5), a CC allele of M0102027 (SEQ ID NO: 11) and an AA allele ofNGMAX008197032 (SEQ ID NO:52). In certain embodiments of these methods,the polymorphic nucleic acid detected in step (b) is detected withmarker M0205350 (SEQ ID NO: 10), M0102027 (SEQ ID NO: 11) orNGMAX008197032 (SEQ ID NO: 52). In certain embodiments of these methods,the polymorphic nucleic acids are detected with marker M0101742 (SEQ IDNO: 5). In certain embodiments of these methods, the polymorphic nucleicacids are detected with marker NGMAX008197032 (SEQ ID NO:52). In certainembodiments of any of the aforementioned methods, the linked polymorphiclocus is detected with a genotypic marker, a phenotypic marker, or both.In certain embodiments of these methods, the linked polymorphic locus isdetected with a marker that is located within about 1000, 500, 100, 40,20, 10, or 5 kilobases (Kb) of the stacked transgenic trait improvementlocus. In certain embodiments of these methods, the linked polymorphiclocus is detected with at least one marker selected from the groupconsisting of asmbl_(—)11856 (SEQ ID NO: 1), TC122822 (SEQ ID NO: 2),BI967232 (SEQ ID NO: 3), M0205537 (SEQ ID NO: 15), M0202715 (SEQ ID NO:16), M0206286 (SEQ ID NO: 17), M0206054 (SEQ ID NO: 18), and M0205375(SEQ ID NO: 19).

Transgenic soybean plants comprising introgressed linkage group Lregions comprising at least one polymorphic allele of at least onemarker in a first sub-region of the linkage group L region that flankedby loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or atleast one polymorphic allele of at least one marker in a secondsub-region of the linkage group L region that is flanked by lociBU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least onepolymorphic allele of at least one marker in a third sub-region of thelinkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) andM0114388 (SEQ ID NO:8), where the polymorphic alleles are associatedwith a stacked transgenic trait improvement locus, and where the plantcomprises: (a) at least two transgenes that contribute to the sametrait; or, (b) at least two transgenes that contribute different traits.In certain embodiments, this same trait is selected from the groupconsisting of resistance to a single herbicide, resistance to an insect,resistance to a nematode, resistance to a fungal disease, resistance toan abiotic stress, an improvement in seed oil quantity, an improvementin seed oil quality, and intrinsic yield increases. In certainembodiments, this different trait is independently selected from thegroup consisting of resistance to one or more herbicide(s), resistanceto one or more insect(s), resistance to one or more nematode(s),resistance to one or more fungal disease(s), resistance to one or moreabiotic stress(es), one or more improvement(s) in seed oil quantity orquantities, one or more improvement(s) in seed oil quality or qualities,intrinsic yield increases, and combinations thereof. In certainembodiments, the polymorphic alleles comprise a TT allele of M0205350(SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CC allele ofM0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032 (SEQ IDNO:52). In certain embodiments, the transgenic plant exhibits a stackedtransgenic trait improvement. In certain embodiments, the transgenicplant further comprises a transgene that confers resistance toglyphosate and exhibits reproductive tolerance to glyphosate. In certainembodiments of any one of the aforementioned methods, the plant furthercomprises at least one of a 2,4-D, glufosinate, bromoxynil, syntheticauxins other than 2,4-D, acetolactate synthase (ALS), acetyl CoAcarboxylase (ACCase), hydroxyphenyl pyruvate dioxygenase (HPPD), orsulfonylurea herbicide resistance transgenes and/or at least onetransgene selected from the group of transgenes conferring insectresistance, nematode resistance, fungal resistance, an improvement inseed oil quantity, an improvement in seed oil quality, abiotic stressresistance, and intrinsic yield increases.

Also provided herein are methods of identifying a soybean plant thatcomprises a genotype associated with stacked transgenic traitimprovement, comprising: detecting in a soybean plant an allele in atleast one genetic locus associated with stacked transgenic traitimprovement, wherein the genetic locus is in a linkage group L genomicregion flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO:12), and denoting that the plant comprises a genotype associated withstacked transgenic trait improvement. In certain embodiments, the methodfurther comprises the step of selecting the denoted plant from apopulation of plants and wherein the detection is performed eitherbefore or after the selection. In certain embodiments, the denoted plantcomprises at least one transgene that confer resistance to an herbicideand is selected for improved tolerance to that herbicide. In certainembodiments, the selection comprises exposing the population of plantsto a dosage of herbicide sufficient to cause a deleterious effect in asusceptible variety comprising the transgene that confers resistance tothe herbicide. In certain embodiments: (i) the plants comprise anherbicide resistance transgene selected from the group consisting of adicamba resistance conferring transgene, a glyphosate resistanceconferring transgene, a 2,4-D resistance conferring transgene, and aglufosinate resistance conferring transgene; and (ii) the plantscomprising the herbicide resistance transgene are exposed to a dosage ofa corresponding herbicide selected from the group consisting of dicamba,glyphosate, glufosinate, and 2,4-D that is sufficient to cause adeleterious effect in a susceptible variety comprising the herbicideresistant transgene that confers resistance to the correspondingherbicide. In certain embodiments, the stacked transgenic traitimprovement is independently selected from the group consisting of animprovement in transgene-mediated resistance to one or moreherbicide(s), an improvement in transgene-mediated resistance to one ormore insect(s), an improvement in transgene-mediated resistance to oneor more nematode(s), an improvement in transgene-mediated resistance toone or more fungal disease(s), an improvement in transgene-mediatedresistance to one or more abiotic stress(es), in one or moreimprovement(s) in transgene-mediated seed oil quantity trait(s), one ormore improvement(s) in seed oil quality trait(s), an improvement intransgene-mediated intrinsic yield increases, and combinations thereof.In certain embodiments, the denoted plant comprises at least oneherbicide resistance transgene and/or at least one insect resistanceconferring transgene that encodes a Bacillus thuringiensis toxin. Incertain embodiments, the denoted plant comprises at least one herbicideresistance transgene selected from the group consisting of a dicambaresistance conferring transgene. a glyphosate resistance conferringtransgene, a 2,4-D resistance conferring transgene, and a glufosinateresistance conferring transgene and/or at least one transgene encoding aproduct that confers insect resistance selected from the groupconsisting of a dsRNA that inhibits a target gene of an insect pest, apatatin, a Bacillus thuringiensis insecticidal protein, a Xenorhabdusinsecticidal protein, a Photorhabdus insecticidal protein, a Bacilluslaterosporous insecticidal protein, a Bacillus sphaericus insecticidalprotein, and a lignin. In certain embodiments of any of the precedingmethods, the genotype associated with stacked transgenic traitimprovement comprises at least one polymorphic allele of at least onemarker in a first sub-region of the linkage group L region that isflanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6)and/or at least one polymorphic allele of at least one marker in asecond sub-region of the linkage group L region that is flanked by lociBU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least onepolymorphic allele of at least one marker in a third sub-region of thelinkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) andM0114388 (SEQ ID NO:8). In certain embodiments of any of the precedingmethods, the genotype associated with stacked transgenic traitimprovement comprises at least one polymorphic allele of at least onemarker in the linkage group L region selected from the group consistingof a TT allele M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ IDNO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and an AA allele ofNGMAX008197032 (SEQ ID NO:52).

Also provided are methods for obtaining a soybean plant comprising inits genome at least one stacked transgenic trait improvement locus,compromising the steps of genotyping a plurality of soybean plants withrespect to at least one genetic locus in a linkage group L genomicregion flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO:12); and selecting a soybean plant comprising in its genome at least onegenetic locus comprising a genotype associated with stacked transgenictrait improvement. In certain embodiments of the methods, the genotypeassociated with stacked transgenic trait improvement comprises at leastone polymorphic allele of at least one marker in a first sub-region ofthe linkage group L region flanked by loci M0205928 (SEQ ID NO: 4) andM0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of atleast one marker in a second sub-region of the linkage group L regionthat is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO:12) and/or at least one polymorphic allele of at least one marker in athird sub-region of the linkage group L region that is flanked by lociBU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8). In certain embodimentsof any of the preceding methods, the genotype associated with stackedtransgenic trait improvement comprises at least one polymorphic alleleof at least one marker in the first linkage group L region, the firstsub-region, or the second sub-region, wherein the marker is selectedfrom the group consisting of a TT allele M0205350 (SEQ ID NO: 10), a TTallele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO:11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certainembodiments of the methods, the plurality of soybean plants comprises apopulation that is obtained by: i) crossing a parent plant comprising atleast one stacked transgenic trait improvement locus with a parent plantcomprising at least one stacked transgenic trait sensitivity locus; or,ii) obtaining seed or progeny from a parental plant segregating for atleast one stacked transgenic trait improvement locus. In certainembodiments of the methods, the population contains plants that compriseat least one transgene that confers resistance to an herbicide and thestacked transgenic trait improvement comprises improved tolerance to acorresponding herbicide. In certain embodiments of any of the precedingmethods, the methods further comprise the step of assaying for thepresence of at least one additional marker, wherein the additionalmarker is either linked or unlinked to the linkage group L genomicregion. In certain embodiments of any of the preceding methods, theplurality of soybean plants, the soybean plant, and/or progeny thereofare exposed to a dosage of herbicide sufficient to cause a deleteriouseffect in a susceptible variety comprising the transgene that confersresistance to the herbicide. In certain embodiments of any of thepreceding methods, a plant that exhibits dicamba tolerance and/orreproductive tolerance to glyphosate and/or glufosinate tolerance and/or2,4-D tolerance is selected. In certain embodiments of any of thepreceding methods, the stacked transgenic trait improvement is selectedfrom the group consisting of an improvement in transgene-mediatedresistance to one or more herbicide(s), an improvement intransgene-mediated resistance to one or more insect(s), an improvementin transgene-mediated resistance to one or more nematode(s), animprovement in transgene-mediated resistance to one or more fungaldisease(s), an improvement in transgene-mediated resistance to one ormore abiotic stress(es), in one or more improvement(s) intransgene-mediated seed oil quantity trait(s), one or moreimprovement(s) in seed oil quality trait(s), an improvement intransgene-mediated intrinsic yield increases, and combinations thereof.

Also provided herein are methods for producing a soybean plantcomprising in its genome at least one introgressed stacked transgenictrait improvement locus comprising the steps of: crossing a firstsoybean plant with a stacked transgenic trait improvement locus with asecond soybean plant comprising: a stacked transgenic trait sensitivitylocus in a first linkage group L genomic region flanked by loci M0205928(SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least onepolymorphic allele of at least one marker in a second sub-region of thelinkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9)and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele ofat least one marker in a third sub-region of the linkage group L regionthat is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8)and at least one linked polymorphic locus not present in the firstsoybean plant to obtain a population segregating for the stackedtransgenic trait improvement loci and the linked polymorphic locus;detecting at least two polymorphic nucleic acids in at least one soybeanplant from the population, wherein at least one of the polymorphicnucleic acids is located in the first linkage group L region and/or thesecond linkage group L region and at least one of the polymorphic aminoacids is a linked polymorphic locus not present in the first soybeanplant; and selecting a soybean plant comprising a genotype associatedwith stacked transgenic trait improvement and at least one linked markerfound in the second soybean plant comprising a stacked transgenic traitsensitivity locus but not in the first soybean plant, thereby obtaininga soybean plant comprising in its genome at least one introgressedstacked transgenic trait improvement locus. In certain embodiments ofthe methods, at least one of the first or the second soybean plantscomprises a transgene that confers resistance to an herbicide. Incertain embodiments of the methods, the population, the selected soybeanplant, and/or progeny of selected soybean plant is exposed to a dosageof herbicide sufficient to cause a deleterious effect in a susceptiblevariety comprising the transgene that confers resistance to acorresponding herbicide. In certain embodiments of the methods, thepolymorphic nucleic acid detected in step (b) is detected with at leastone marker selected from the group consisting of M0205350 (SEQ ID NO:10), M0101742 (SEQ ID NO: 5), M0102027 (SEQ ID NO: 11), andNGMAX008197032 (SEQ ID NO:52). In certain embodiments of the methods,the polymorphic nucleic acid detected in step (b) comprises a TT alleleof M0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), aCC allele of M0102027 (SEQ ID NO: 11), and an AA allele ofNGMAX008197032 (SEQ ID NO:52). In certain embodiments of the methods,the polymorphic nucleic acid detected in step (b) is detected withmarker M0205350 (SEQ ID NO: 10), M0102027 (SEQ ID NO: 11), or markerNGMAX008197032 (SEQ ID NO:52). In certain embodiments of the methods,the polymorphic nucleic acids are detected with marker M0101742 (SEQ IDNO: 5). In certain embodiments of any of the preceding methods, thelinked polymorphic locus is detected with a genotypic marker, aphenotypic marker, or both. In certain embodiments, the linkedpolymorphic locus is detected with a marker that is located within about1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of the stackedtransgenic trait improvement locus. In certain embodiments, the linkedpolymorphic locus is detected with at least one marker selected from thegroup consisting of asmbl_(—)11856 (SEQ ID NO: 1), TC122822 (SEQ ID NO:2), BI967232 (SEQ ID NO: 3), M0205537 (SEQ ID NO: 15), M0202715 (SEQ IDNO: 16), M0206286 (SEQ ID NO: 17), M0206054 (SEQ ID NO:18), and M0205375(SEQ ID NO: 19).

Also provided are transgenic soybean plants comprising introgressedlinkage group L regions comprising at least one polymorphic allele of atleast one marker in a first sub-region of the linkage group L regionthat flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6)and/or at least one polymorphic allele of at least one marker in asecond sub-region of the linkage group L region that is flanked by lociBU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least onepolymorphic allele of at least one marker in a third sub-region of thelinkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) andM0114388 (SEQ ID NO:8), wherein the polymorphic alleles are associatedwith stacked transgenic trait improvement and wherein the plantcomprises at least one transgene. In certain embodiments, the transgeneconfers resistance to an herbicide. In certain embodiments, thepolymorphic alleles comprise a TT allele of M0205350 (SEQ ID NO: 10), aTT allele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ IDNO: 11), and an AA allele of NGMAX008197032 (SEQ ID NO:52). In certainembodiments of any of the preceding methods, the plant exhibitstolerance to at least one herbicide. In certain embodiments, the plantcomprises: i) a transgene that confers resistance to glyphosate andexhibits reproductive tolerance to glyphosate; and/or (ii) a dicambaresistance conferring transgene and exhibits dicamba tolerance; and/or(iii) a glufosinate resistance conferring transgene and exhibitsglufosinate tolerance; and/or (iv) a 2,4-D resistance conferringtransgene and exhibits 2,4-D tolerance. In certain embodiments, theplant comprises at least one transgene conferring resistance to aherbicide selected from the group consisting of dicamba, 2,4-D,glufosinate, bromoxynil, synthetic auxins other than 2,4-D, acetolactatesynthase (ALS), acetyl CoA carboxylase (ACCase), hydroxyphenyl pyruvatedioxygenase (HPPD), and a sulfonylurea herbicide and/or at least onetransgene selected from the group of transgenes conferring insectresistance, nematode resistance, fungal resistance, an improvement inseed oil quantity, an improvement in seed oil quality, abiotic stressresistance, and intrinsic yield increases. In certain embodiments, theplant comprises at least one herbicide resistance transgene and/or atleast one insect resistance conferring transgene that encodes a Bacillusthuringiensis toxin. In certain embodiments, the plant comprises atleast one herbicide resistance transgene selected from the groupconsisting of a dicamba resistance conferring transgene a glyphosateresistance conferring transgene, a 2,4-D resistance conferringtransgene, and a glufosinate resistance conferring transgene and/or atleast one transgene encoding a product that confers insect resistanceselected from the group consisting of a dsRNA that inhibits a targetgene of an insect pest, a patatin, a Bacillus thuringiensis insecticidalprotein, a Xenorhabdus insecticidal protein, a Photorhabdus insecticidalprotein, a Bacillus laterosporous insecticidal protein, a Bacillussphaericus insecticidal protein, and a lignin.

Also provided herein are methods of identifying a transgenic soybeanplant that comprises a genotype associated with stacked transgenic traitimprovement, the method comprising: (a) scoring at least one transgenicplant in a population of transgenic soybean plants that had been exposedto dicamba for dicamba tolerance, the plants having a transgene thatconfers resistance to dicamba; and, (b) selecting a transgenic plantthat exhibits dicamba tolerance, thereby identifying a transgenicsoybean plant that comprises a genotype associated with stackedtransgenic trait improvement. In certain embodiments, the population issegregating for to at least one genetic locus in a linkage group Lgenomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQID NO: 12) that is associated with stacked transgenic trait improvement.In certain embodiments, the method further comprises genotyping theselected soybean plant with respect to at least one genetic locus in alinkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4)and BU765955 (SEQ ID NO: 12). In certain embodiments, the selectedtransgenic plant further comprises a transgene that confers resistanceto glyphosate and the selected transgenic plant or progeny thereof isscored for reproductive tolerance to glyphosate following exposure toglyphosate. In certain embodiments of any of the preceding methods, themethods further comprise exposing the population of transgenic soybeanplants to dicamba. In certain embodiments of any of the precedingmethods, dicamba tolerance is scored by determining a reduction inmalformation when compared to a dicamba sensitive transgenic plant thatcomprises the transgene that confers resistance to dicamba. In certainembodiments of any of the preceding methods, the stacked transgenictrait improvement is selected from the group consisting of animprovement in transgene-mediated resistance to one or moreherbicide(s), an improvement in transgene-mediated resistance to one ormore insect(s), an improvement in transgene-mediated resistance to oneor more nematode(s), an improvement in transgene-mediated resistance toone or more fungal disease(s), an improvement in transgene-mediatedresistance to one or more abiotic stress(es), in one or moreimprovement(s) in transgene-mediated seed oil quantity trait(s), one ormore improvement(s) in seed oil quality trait(s), an improvement intransgene-mediated intrinsic yield increases, and combinations thereof.In certain embodiments of any of the preceding methods, the selectedplant comprises at least one additional herbicide resistance transgeneselected from the group consisting of a glyphosate resistance conferringtransgene, a 2,4-D resistance conferring transgene, and a glufosinateresistance conferring transgene and/or at least transgene encoding aproduct that confers insect resistance selected from the groupconsisting of a dsRNA that inhibits a target gene of an insect pest, apatatin, a Bacillus thuringiensis insecticidal protein, a Xenorhabdusinsecticidal protein, a Photorhabdus insecticidal protein, a Bacilluslaterosporous insecticidal protein, a Bacillus sphaericus insecticidalprotein, and a lignin.

Also provided herein are methods of identifying a transgenic soybeanplant that comprises a genotype associated with stacked transgenic traitimprovement, comprising: (a) scoring at least one plant in a populationof transgenic soybean plants that had been exposed to glyphosate forreproductive tolerance to glyphosate, wherein the plants comprise atransgene that confers resistance to glyphosate; and, (b) selecting atransgenic plant that exhibits reproductive tolerance to glyphosate,thereby identifying a transgenic soybean plant that comprises a genotypeassociated with stacked transgenic trait improvement. In certainembodiments, the population is segregating for to at least one geneticlocus in a linkage group L genomic region flanked by loci M0205928 (SEQID NO: 4) and BU765955 (SEQ ID NO: 12) that is associated with stackedtransgenic trait improvement. In certain embodiments, the method furthercomprises genotyping the selected soybean plant with respect to at leastone genetic locus in a linkage group L genomic region flanked by lociM0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12). In certainembodiments of any of the preceding methods, the selected transgenicplant further comprises a transgene that confers resistance to dicambaand the selected transgenic plant or progeny thereof is scored fortolerance to dicamba following exposure to dicamba. In certainembodiments of any of the preceding methods, the methods furthercomprise exposing the population of transgenic soybean plants toglyphosate. In certain embodiments of any of the preceding methods,glyphosate reproductive tolerance is scored by determining a reductionin sterility when compared to a transgenic plant that exhibitsglyphosate reproductive sensitivity and comprises the transgene thatconfers resistance to glyphosate. In certain embodiments of any of thepreceding methods, the stacked transgenic trait improvement is selectedfrom the group consisting of an improvement in transgene-mediatedresistance to one or more herbicide(s), an improvement intransgene-mediated resistance to one or more insect(s), an improvementin transgene-mediated resistance to one or more nematode(s), animprovement in transgene-mediated resistance to one or more fungaldisease(s), an improvement in transgene-mediated resistance to one ormore abiotic stress(es), in one or more improvement(s) intransgene-mediated seed oil quantity trait(s), one or moreimprovement(s) in seed oil quality trait(s), an improvement intransgene-mediated intrinsic yield increases, and combinations thereof.In certain embodiments of any of the preceding methods, the selectedplant comprises at least one additional herbicide resistance transgeneselected from the group consisting of a dicamba resistance conferringtransgene, a 2,4-D resistance conferring transgene, and a glufosinateresistance conferring transgene and/or at least one transgene encoding aproduct that confers insect resistance selected from the groupconsisting of a dsRNA that inhibits a target gene of an insect pest, apatatin, a Bacillus thuringiensis insecticidal protein, a Xenorhabdusinsecticidal protein, a Photorhabdus insecticidal protein, a Bacilluslaterosporous insecticidal protein, a Bacillus sphaericus insecticidalprotein, and a lignin.

Also provided are methods of obtaining a transgenic soybean plant thatcomprises a genotype associated with stacked transgenic traitimprovement, the methods comprising: exposing a population of transgenicsoybean plants to an herbicide, wherein the plants have a transgene thatconfers resistance to the herbicide; observing herbicide toleranceexhibited by one or more soybean plants following exposure to theherbicide; and, (c) selecting a transgenic plant that exhibitsherbicidetolerance, thereby obtaining a transgenic soybean plant thatcomprises a genotype associated with stacked transgenic traitimprovement. In certain embodiments, the population is segregating forto at least one genetic locus in a linkage group L genomic regionflanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12)that is associated with stacked transgenic trait improvement. In certainembodiments, the method further comprises genotyping the selectedsoybean plant with respect to at least one genetic locus in a linkagegroup L genomic region flanked by loci M0205928 (SEQ ID NO: 4) andBU765955 (SEQ ID NO: 12). In certain embodiments of any of the precedingmethods, the transgene that confers resistance to the herbicide isselected from the group consisting of a dicamba resistance conferringtransgene, a glyphosate resistance conferring transgene, a 2,4-Dresistance conferring transgene, and a glufosinate resistance conferringtransgene and the plants are exposed to the corresponding herbicide. Incertain embodiments of any of the preceding methods, the transgeneconfers resistance to glyphosate and the selected transgenic plant orprogeny thereof is scored for reproductive tolerance to glyphosatefollowing exposure to glyphosate. In certain embodiments of any of thepreceeding methods, the transgene confers resistance to dicamba and theselected transgenic plant or progeny thereof are scored for dicambatolerance.

Also provided herein are methods of identifying a transgenic soybeanplant that comprises a genotype associated with reproductive toleranceto glyphosate, the method comprising: (a) scoring at least onetransgenic plant in a population of transgenic soybean plants that hadbeen exposed to dicamba for dicamba tolerance, the plants having atransgene that confers resistance to dicamba; and, (b) selecting atransgenic plant that exhibits dicamba tolerance, thereby identifying atransgenic soybean plant that comprises a genotype associated withreproductive tolerance to glyphosate. In certain embodiments of themethods, the population is segregating for to at least one genetic locusin a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO:4) and BU765955 (SEQ ID NO: 12) that is associated with dicambatolerance. In certain embodiments of the methods, the methods furthercomprise genotyping the selected soybean plant with respect to at leastone genetic locus in a linkage group L genomic region flanked by lociM0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12). In certainembodiments of any of the aforementioned methods, the selectedtransgenic plant further comprises a transgene that confers resistanceto glyphosate and wherein the selected transgenic plant or progenythereof is scored for reproductive tolerance to glyphosate followingexposure to glyphosate. In certain embodiments of any of theaforementioned methods, the methods further comprise exposing thepopulation of transgenic soybean plants to dicamba. In certainembodiments of any of the aforementioned methods, the dicamba toleranceis scored by determining a reduction in malformation when compared to adicamba sensitive transgenic plant that comprises the transgene thatconfers resistance to dicamba.

Also provided herein are methods of identifying a transgenic soybeanplant that comprises a genotype associated with tolerance to dicamba,comprising: (a) scoring at least one plant in a population of transgenicsoybean plants that had been exposed to glyphosate for reproductivetolerance to glyphosate, wherein the plants comprise a transgene thatconfers resistance to glyphosate; and, (b) selecting a transgenic plantthat exhibits reproductive tolerance to glyphosate, thereby identifyinga transgenic soybean plant that comprises a genotype associated withdicamba tolerance. In certain embodiments of the methods, the populationis segregating for to at least one genetic locus in a linkage group Lgenomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQID NO: 12) that is associated with dicamba tolerance. In certainembodiments of the methods, the method further comprises genotyping theselected soybean plant with respect to at least one genetic locus in alinkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4)and BU765955 (SEQ ID NO: 12). In certain embodiments of any of theaforementioned methods, the selected transgenic plant further comprisesa transgene that confers resistance to dicamba and wherein the selectedtransgenic plant or progeny thereof is scored for tolerance to dicambafollowing exposure to dicamba. In certain embodiments of any of theaforementioned methods, the methods further comprise exposing thepopulation of transgenic soybean plants to glyphosate. In certainembodiments of any of the aforementioned methods, the glyphosatereproductive tolerance is scored by determining a reduction in sterilitywhen compared to a transgenic plant that exhibits glyphosatereproductive sensitivity and comprises the transgene that confersresistance to glyphosate.

Also provided herein are methods of obtaining a transgenic soybean plantthat comprises a genotype associated with reproductive tolerance toglyphosate, the methods comprising: (a) exposing a population oftransgenic soybean plants to dicamba, wherein the plants have atransgene that confers resistance to dicamba; (b) observing dicambatolerance exhibited by one or more soybean plants following exposure todicamba; and, (c) selecting a transgenic plant that exhibits dicambatolerance, thereby obtaining a transgenic soybean plant that comprises agenotype associated with reproductive tolerance to glyphosate. Incertain embodiments of the methods, the population is segregating for toat least one genetic locus in a linkage group L genomic region flankedby loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12) that isassociated with dicamba tolerance. In certain embodiments of themethods, the methods further comprise genotyping the selected soybeanplant with respect to at least one genetic locus in a linkage group Lgenomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQID NO: 12). In certain embodiments of any of the aforementioned methods,the selected transgenic plant further comprises a transgene that confersresistance to glyphosate and the selected transgenic plant or progenythereof is scored for reproductive tolerance to glyphosate followingexposure to glyphosate. In certain embodiments of any of theaforementioned methods, the dicamba tolerance is scored by determining areduction in malformation when compared to a dicamba sensitivetransgenic plant that comprises the transgene that confers resistance todicamba. Further areas of applicability will become apparent from thedescription provided herein. It should be understood that thedescription and specific examples are intended for purposes ofillustration only and are not intended to limit the scope of the presentdisclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a bar graph of the percent injury at 7 days after treatmentwith Dicamba (y-axis) for various favorable and unfavorable soybeanplant haplotypes containing a dicamba resistance conferring transgene(x-axis). The favorable haplotypes are haplotypes that are notassociated with the dicamba intolerance trait and the unfavorablehaplotypes are associated with the dicamba intolerance trait. In thegraph, “Fav Hap is “Favorable Haplotype” and “Unf Hap” is “UnfavorableHaplotype”. The data show that presence of the favorable haplotype isassociated with improved tolerance to dicamba.

FIG. 2 shows a bar graph of the percent injury at 7 days after treatmentwith either a single treatment (V6 stage, solid bars) or two treatments(V3+V6 stages, open bars) of Dicamba (y-axis) for various favorable andunfavorable soybean plant haplotypes (x-axis) containing a dicambaresistance conferring transgene (x-axis). In the graph, “Fav Hap is“Favorable Haplotype” and “Unf Hap” is “Unfavorable Haplotype”. The datashow that favorable haplotypes can be selected with either a singletreatment at the V6 stageor two treatments at the V3 and V6 stages.

DETAILED DESCRIPTION Definitions

As used herein, an “allele” refers to one of two or more alternativeforms of a genomic sequence at a given locus on a chromosome. When allthe alleles present at a given locus on a chromosome are the same, thatplant is homozygous at that locus. If the alleles present at a givenlocus on a chromosome differ, that plant is heterozygous at that locus.

As used herein, the term “denoting” when used in reference to a plantgenotype refers to any method whereby a plant is indicated to have acertain genotype. Such indications of a certain genotype include, butare not limited to, any method where a plant is physically marked ortagged. Physical markings or tags that can be used include, but notlimited to, a barcode, a radio-frequency identification (RFID), a labelor the like. Indications of a certain genotype also include, but are notlimited to, any entry into any type of written or electronic databasewhereby the plant's genotype is provided.

A “locus” is a position on a genomic sequence that is usually found by apoint of reference; e.g., a short DNA sequence that is a gene, or partof a gene or intergenic region. A locus may refer to a nucleotideposition at a reference point on a chromosome, such as a position fromthe end of the chromosome.

As used herein, “linkage group L” corresponds to the soybean linkagegroup L described in Choi, et al., Genetics. 2007 May; 176(1): 685-696.Linkage group L, as used herein, also corresponds to soybean chromosome19 (as described on the World Wide Web at soybase.org/LG2Xsome.php). Asused herein, “polymorphism” means the presence of one or more variationsof a nucleic acid sequence at one or more loci in a population of atleast two members. The variation can comprise but is not limited to oneor more nucleotide base substitutions, the insertion of one or morenucleotides, a nucleotide sequence inversion, and/or the deletion of oneor more nucleotides.

As used herein, the term “single nucleotide polymorphism,” also referredto by the abbreviation “SNP,” means a polymorphism at a single sitewherein the polymorphism constitutes any or all of a single base pairchange, an insertion of one or more base pairs, and/or a deletion of oneor more base pairs.

As used herein, “marker” means a detectable characteristic that can beused to discriminate between organisms. Examples of such characteristicsinclude, but are not limited to, genetic markers, biochemical markers,fermentation yield, fermentation efficiency, energy yield, secondarycompounds, metabolites, morphological characteristics, and agronomiccharacteristics.

As used herein, “marker assay” means a method for detecting apolymorphism at a particular locus using a particular method. Markerassays thus include, but are not limited to, measurement of at least onephenotype (such as seed color, flower color, or other visuallydetectable trait as well as any biochemical trait), restriction fragmentlength polymorphism (RFLP), single base extension, electrophoresis,sequence alignment, allelic specific oligonucleotide hybridization(ASO), random amplified polymorphic DNA (RAPD), microarray-basedpolymorphism detection technologies, and the like.

As used herein, “genotype” means the genetic component of the phenotypeand it can be indirectly characterized using markers or directlycharacterized by nucleic acid sequencing.

As used herein, the term “introgressed”, when used in reference to agenetic locus, refers to a genetic locus that has been introduced into anew genetic background. Introgression of a genetic locus can thus beachieved through both plant breeding methods or by molecular geneticmethods. Such molecular genetic methods include, but are not limited to,various plant transformation techniques and/or methods that provide forhomologous recombination, non-homologous recombination, site-specificrecombination, and/or genomic modifications that provide for locussubstitution or locus conversion. In certain embodiments, introgressioncould thus be achieved by substitution of a dicamba intolerance locuswith a corresponding dicamba tolerance locus or by conversion of a locusfrom a dicamba intolerance genotype to a dicamba tolerance genotype.

As used herein, “phenotype” means the detectable characteristics of acell or organism which can be influenced by gene expression.

As used herein, “linkage” refers to relative frequency at which types ofgametes are produced in a cross. For example, if locus A has genes “A”or “a” and locus B has genes “B” or “b” and a cross between parent Iwith AABB and parent B with aabb will produce four possible gameteswhere the genes are segregated into AB, Ab, aB and ab. The nullexpectation is that there will be independent equal segregation intoeach of the four possible genotypes, i.e. with no linkage ¼ of thegametes will of each genotype. Segregation of gametes into a genotypesdiffering from ¼ are attributed to linkage.

As used herein, the termed “linked”, when used in the context of markersand/or genomic regions, means that the markers and/or genomic regionsare located on the same linkage group or chromosome.

As used herein, a “nucleic acid molecule,” be it a naturally occurringmolecule or otherwise may be “substantially purified”, if desired,referring to a molecule separated from substantially all other moleculesnormally associated with it in its native state. More preferably, asubstantially purified molecule is the predominant species present in apreparation. A substantially purified molecule may be at least about 60%free, preferably at least about 75% free, more preferably at least about90% free, and most preferably at least about 95% free from the othermolecules (exclusive of solvent) present in the natural mixture. Theterm “substantially purified” is not intended to encompass moleculespresent in their native state.

As used herein, “quantitative trait locus (QTL)” means a locus thatcontrols to some degree numerically representable traits that areusually continuously distributed. As used herein, the term “transgene”means nucleic acid molecules in the form of DNA, such as cDNA or genomicDNA, and RNA, such as mRNA or microRNA, which may be single or doublestranded.

As used herein, the term “event”, when used in the context of describinga transgenic plant, refers to a particular transformed plant line. In atypical transgenic breeding program, a transformation constructresponsible for a trait is introduced into the genome via atransformation method. Numerous independent transformants (events) areusually generated for each construct. These events are evaluated toselect those with superior performance.

As used herein, the term “soybean” means Glycine max and includes allplant varieties that can be bred with soybean, including wild soybeanspecies. In certain embodiments, soybean plants from the species Glycinemax and the subspecies Glycine max L. ssp. max or Glycine max ssp.formosana can be genotyped using the compositions and methods of thepresent invention. In an additional aspect, the soybean plant is fromthe species Glycine soja, otherwise known as wild soybean, can begenotyped using these compositions and methods. Alternatively, soybeangermplasm derived from any of Glycine max, Glycine max L. ssp. max,Glycine max ssp. Formosana, and/or Glycine soja can be genotyped usingcompositions and methods provided herein.

As used herein, the term “bulk” refers to a method of managing asegregating population during inbreeding that involves growing thepopulation in a bulk plot, harvesting the self-pollinated seed of plantsin bulk, and using a sample of the bulk to plant the next generation.

As used herein, the phrase “transgene that confers tolerance to dicamba”refers to the ability of a transgene to provide a soybean plant capableof surviving exposure to dicamba at a rate of about 0.5 pounds of acidequivalent per acre of dicamba acid to about 1.5 pounds of acidequivalent per acre of dicamba acid applied at either pre-emergenceand/or postemergence. Transgenic plants comprising a transgene thatconfers tolerance to dicamba can exhibit, either a “dicamba tolerant”phenotype in certain soybean germplasms or a “dicamba sensitive”phenotype in other distinct soybean germplasms when exposed to dicamba.

As used herein, the phrase “dicamba intolerant” refers to undesirablephenotypic traits observed in certain soybean germplasms that comprise atransgene that confers resistance to dicamba after exposure to dicambaat a rate of about 0.5 pounds of acid equivalent per acre of dicambaacid to about 1.5 pounds of acid equivalent per acre of dicamba acid.Such undesirable phenotypic traits include, but are not limited to,pronounced bending/twisting of the main stem and petioles, necrosis ofthe upper nodes and petioles, and/or limitation of new growth.

As used herein, the phrase “dicamba tolerant” refers to either theabsence or reduction of undesirable phenotypic traits observed afterexposure to dicamba in “dicamba intolerant” soybean germplasms thatcomprise a transgene that confers resistance to dicamba.

As used herein, the term “comprising” means “including but not limitedto”.

As used herein, the terms “scoring” or “score”, refer to any qualitive,semi-quantitive, or quantitive method for determining the presence,absence, and/or the partial presence or absence, of a phenotypic trait.

As used herein, the phrase “susceptible variety”, when used in referenceto herbicide tolerance in a soybean plant comprising a transgene thatconfers resistance to that herbicide, refers to a soybean variety thatallele(s) of the stacked transgenic trait improvement locus that do notconfer such stacked transgenic trait improvements. “Susceptiblevarieties’ are also referred to herein as “sensitive varieties” in thecontext of herbicide tolerance in a soybean plant comprising a transgenethat confers resistance to that herbicide.

As used herein, the phrase “corresponding herbicide”, when used inreference to a transgene that confers herbicide resistance, refers tothe herbicide that the transgene confers resistance to. Thus, acorresponding herbicide for a transgene that confers resistance toglyphosate, dicamba, 2,4-D, or glufosinate is respectively glyphosate,dicamba, 2,4-D, or glufosinate.

DESCRIPTION

In accordance with the present invention, Applicants have discoveredgenomic regions, associated markers, and associated methods foridentifying and associating genotypes that effect the levels of dicambatolerance observed in soybean plants comprising a transgene that confersresistance to dicamba. Dicamba (3,6-dichloro-o-anisic acid) is a usefulbroad spectrum herbicide for controlling weeds. For example, in oneembodiment, a method of the invention comprises screening a plurality oftransgenic germplasm entries displaying a heritable variation for atleast one transgene mediated dicamba resistance trait wherein theheritable variation is linked to at least one genotype; and associatingat least one genotype from the transgenic germplasm entries to at leastone dicamba tolerance trait. In another embodiment, a method of theinvention comprises crossing at least two germplasm entries with a testgermplasm entry for the evaluation of performance of at least onedicamba tolerance trait in order to determine preferred crossingschemes. The methods of the present invention can be used withtraditional breeding techniques as described below to more efficientlyscreen and identify genotypes affecting a dicamba tolerance trait.

The use of markers to infer a phenotype of interest results in theeconomization of a breeding program by substituting costly,time-intensive phenotyping assays with genotyping assays. Further,breeding programs can be designed to explicitly drive the frequency ofspecific, favorable phenotypes by targeting particular genotypes (U.S.Pat. No. 6,399,855). Fidelity of these associations may be monitoredcontinuously to ensure maintained predictive ability and, thus, informedbreeding decisions (US Patent Application 2005/0015827). In this case,costly, time-intensive phenotyping assays required for determining if aplant or plants contains a genomic region associated with a “dicambatolerance” or “Dicamba intolerance” phenotype can be supplanted bygenotypic assays that provide for identification of a plant or plantsthat contain the desired genomic region that confers dicamba tolerance.

A Genomic Region Associated with a Dicamba Tolerance Phenotype

Provided herewith is a soybean genomic region that is shown herein to beassociated with a desirable dicamba tolerance phenotype when present incertain allelic forms and when combined with certain transgenic locithat confer dicamba tolerance.

A soybean genomic region provided that can be associated with adesirable dicamba tolerance phenotype when present in certain allelicforms is located on the telomere proximal end of the short arm ofsoybean linkage group L (chromosome 19). A series of markers useful inpracticing the methods of this invention are provided herewith inTable 1. Additional markers useful in the practice of the invention areprovided herewith in Table 2 of the Specification, which is incorporatedherewith by reference in its entirety. Table 2 provides the Table 1markers, additional nucleic acid markers or loci that have beendisclosed in various databases, the relative positions of the markers ona physical map of linkage group L (soybean chromosome 19), and sourcesfor the markers.

TABLE 1 Markers spanning a genomic region associated with a desirabledicamba tolerance phenotype Allelic form(s) Marker or Locus SEQ ID MapAssociated with Name NO: Position ¹ Dicamba Tolerance ² asmbl_11856 116506 TC122822 2 32108 BI967232 3 66686 M0205928 4 92526 M0101742³ 5112836 TT⁶ M0129138 6 114013 BU551345 7 116147 M0114388 8 380897BU551363 9 422447 M0205350⁴ 10 423935 TT⁷ M0102027⁵ 11 466558 CC⁸BU765955 12 474316 M0093116 13 805580 M0129925 14 831128 M0205537 15890254 M0202715 16 921431 M0206286 17 1209977 M0206054 18 1465354M0205375 19 2009800 NGMAX008197032⁹ 52 314997 AA¹⁰ ¹ The relativepositions of the approximate middle position of the listed markers orloci based on nucleotide positions on a physical map of soybean linkagegroup L (chromosome 19) of Table 2 are provided where nucleotideposition 0 (zero) is telomere proximal and nucleotide position 2009800is centromere proximal. Polymorphic nucleotide bases are designated inthe sequence listing provided herewith according to the WIPO StandardST.25 (1998), Table 1, as follows: r = g or a (purine); y = t/u or c(pyrimidine); m = a or c; (amino); k = g or t/u (keto); s = g or c(strong interactions 3 H-bonds); w = a or t/u (weak interactions2H-bonds); b = g or c or t/u (not a); d = a or g or t/u (not c); h = aor c or t/u (not g); v = a or g or c (not t, not u); and n = a or g or cor t/u (unknown, or other; any.) ² Both the maternal and paternalalleles of the single nucleotide polymorphisms that can be associatedwith a dicamba tolerance phenotype are shown. ³The identifiedpolymorphic allele of marker M0101742 is located at nucleotide 1206 ofSEQ ID NO: 5. ⁴The identified polymorphic allele of marker M0205350 islocated at nucleotide 148 of SEQ ID NO: 10. ⁵The identified polymorphicallele of marker M0102027is located at nucleotide 349 of SEQ ID NO: 11.⁶The identified polymorphic allele of marker M0101742 “TT” can beassociated with a dicamba tolerance phenotype when the identifiedpolymorphic alleles of the other markers are: “TT” for M0205350 and, incertain embodiments, “CC” for M0102027. ⁷The identified polymorphicallele of marker M020350 “TT” can be associated with a dicamba tolerancephenotype when the identified polymorphic alleles of the other markersare: “TT” for M0101742 and, in certain embodiments, “CC” for M0102027.⁸In certain embodiments, the identified polymorphic allele “CC” formarker M0102027 can be associated with a dicamba tolerance phenotypewhen the identified polymorphic alleles of the other markers are: “TT”for M0101742 and “TT” for M020350. ⁹The identified polymorphic allele ofmarker NGMAX008197032 is located at nucleotide 201 of SEQ ID NO: 52.¹⁰In certain embodiments, the identified polymorphic allele of markerNGMAX008197032 “AA” can be associated with a dicamba tolerance phenotypewhen the identified polymorphic alleles of the other markers are: “TT”for M0205350 and, in certain embodiments, “CC” for M0102027, and “TT”for M0101742.

Also provided herein are sub-regions of the linkage group L region thatis flanked by loci M0205928 (SEQ ID NO: 4) and BU765995 (SEQ ID NO: 12)that are associated with a dicamba tolerance phenotype. A firstsub-region of the linkage group L region associated with a dicambatolerance phenotype is flanked by loci M0205928 (SEQ ID NO: 4) andM0129138 (SEQ ID NO: 6). These loci flank a first sub-region that spanstelomere proximal nucleotide 92334 to centromere proximal nucleotide113494 in the physical map of linkage group L provided in Table 2 of thespecification. Polymorphisms located in this first sub-region that areassociated with a dicamba tolerance phenotype can be detected withmarkers that include, but are not limited to, M0101742 (SEQ ID NO: 5). Asecond sub-region of the linkage group L region associated with adicamba tolerance phenotype is flanked by loci BU551363 (SEQ ID NO: 9)and BU765955 (SEQ ID NO: 12). These loci flank the second sub-regionthat spans telomere proximal nucleotide 422447 to centromere proximalnucleotide 474316 in the physical map of linkage group L provided inTable 2 of the specification. Polymorphisms located in this secondsub-region that are associated with a dicamba tolerance phenotype can bedetected with markers that include, but are not limited to, M0205350(SEQ ID NO: 10) or M0102027 (SEQ ID NO: 11). A third sub-region of thelinkage group L region associated with a dicamba tolerance phenotype isflanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8). Theseloci flank the second sub-region that spans telomere proximal nucleotide115,956 to centromere proximal nucleotide 380,486 in the physical map oflinkage group L provided in Table 2 of the specification. Polymorphismslocated in this third sub-region that are associated with a dicambatolerance phenotype can be detected with markers that include, but arenot limited to, NGMAX008197032 (SEQ ID NO:52). In certain embodiments ofinvention, a polymorphism associated with a dicamba tolerant phenotypeis detected in only one of these sub-regions. In other embodiments ofthe invention, at least one polymorphism associated with a dicambatolerant phenotype is detected in any two of these sub-regions. Thus, amarker including, but not limited to, M0101742 (SEQ ID NO: 5) can beused either independently of, or in combination with, one or moremarkers selected from the group consisting of M0205350 (SEQ ID NO: 10)and/or M0102027 (SEQ ID NO: 11) to detect polymorphisms associated witha dicamba tolerance phenotype. In certain embodiments, a markerincluding, but not limited to, M0101742 (SEQ ID NO: 5) can be usedeither independently of, or in combination with, marker NGMAX008197032(SEQ ID NO:52) to detect polymorphisms associated with a dicambatolerance phenotype. In certain embodiments, a marker including, but notlimited to, marker NGMAX008197032 (SEQ ID NO:52) can be used eitherindependently of, or in combination with, one or more markers selectedfrom the group consisting of M0205350 (SEQ ID NO: 10) and/or M0102027(SEQ ID NO: 11) to detect polymorphisms associated with a dicambatolerance phenotype. In certain embodiments, a polymorphism in the firstsub-region is detected with marker M0101742 (SEQ ID NO: 5) and apolymorphism in the second sub-region is detected with markers M0205350(SEQ ID NO: 10) and/or M0102027 (SEQ ID NO: 11). In certain embodiments,a polymorphism in the first sub-region is detected with marker M0101742(SEQ ID NO: 5) and a polymorphism in the third sub-region is detectedwith marker NGMAX008197032 (SEQ ID NO: 52). In certain embodiments, thealleles of these markers associated with dicamba tolerance are a TTallele M0101742 (SEQ ID NO: 5), a TT allele of M0205350 (SEQ ID NO: 10),and, in certain embodiments, a CC allele of M0102027 (SEQ ID NO: 11),and an AA allele of NGMAX008197032 (SEQ ID NO:52).

Additional genetic markers can be used either in conjunction with themarkers provided in Table 1 and/or Table 2 or independently of themarkers provided in Table 1 and/or Table 2 to practice the methods ofthe instant invention. Publicly available marker databases from whichuseful markers can be obtained include, but are not limited to, thesoybase.org website on the internet (World Wide Web) that isadministered by the United States Agricultural Research Service, theUnited States Department of Agriculture, and Iowa State University.Additional soybean markers that can be used and that have been describedin the literature include, but are not limited to, Hyten et al., BMCGenomics. 11:38, 2010; Choi et al., Genetics. 176(1):685-96, 2007; Yoonet al., Theor Appl Genet. 2007 March; 114(5):885-99; and Hyten et al.Crop Sci. 2010 50: 960-968. Given the provision herein of a genomicregion on linkage group L (chromosome 19) delimited or flanked by thetelomere proximal locus M0205928 (SEQ ID NO: 4) of Table 2 and thecentromere proximal locus BU765955 (SEQ ID NO: 12) of Table 2 as well asan assortment of soybean germplasms exhibiting either a “dicambaintolerant” or “dicamba tolerant” phenotype, additional markers locatedeither within or near this genomic region that are associated with thesephenotypes can be obtained by merely typing the new markers in thevarious germplasms provided herewith. The genomic region on linkagegroup L (chromosome 19) delimited or flanked by the telomere proximallocus M0205928 (SEQ ID NO: 5) of Table 2 and the centromere proximallocus BU765955 (SEQ ID NO: 12) of Table 2 can also be mapped relative tomarkers provided in any publicly available or other soybean physical orgenetic map to place this genetic locus on that map.

Identification of Plants Exhibiting the “Dicamba Intolerance” or“Dicamba Tolerance” Phenotype

To observe the presence or absence of the “dicamba intolerance” ordicamba tolerance phenotypes, transgenic soybean plants comprising atransgene that confers resistance to dicamba are typically exposed inearly to mid-vegetative growth stages to one or more high doses ofdicamba. Typical doses of dicamba that can elicit a dicamba intolerancephenotype can range from about a 2-fold label application rate of acommercially available dicamba formulation to about a 3-fold labelapplication rate of a commercially available dicamba formulation. Interms of acid equivalents of dicamba acid applied, typical doses ofdicamba that can elicit a dicamba intolerance phenotype can range froman application rate of about 1.0 pounds of acid equivalent per acre ofdicamba acid to about 1.5 pounds of acid equivalent per acre of dicambaacid when the indicated amounts of dicamba acid are provided in either acommercially available dicamba formulation or when the indicated amountsof dicamba acid is provided in a similar formulation suitable forapplication to dicamba-tolerant crops. Commercially available dicambaformulations that can be used include, but are not limited to, Clarity®(BASF, NC, USA); Banvel®, Banvel M®, Banvel II®, Banvel SGF®, orVanquish® (Syngenta, Wilmington, Del., USA); or Rifle® (LovelandProducts, Inc., Loveland, Colo., USA). In certain embodiments, thecommercially available dicamba formulation used is Clarity®. In certainembodiments, doses of dicamba that can elicit a dicamba intolerancephenotype can range from about a 2 fold application rate of about 0.25gallons per acre Clarity® to about a three fold application rate ofabout 0.375 gallons per acre per acre Clarity®.

The dicamba intolerance phenotype can be observed approximately a weekafter herbicide application in certain soybean varieties comprising thetransgene that confers resistance to dicamba. Dicamba is typicallyapplied during pre and post-emergent vegetative growth stages. Incertain embodiments of these methods, dicamba can be applied in weeklyintervals (i.e. once a week) for any of 2, 3, 4 or more successive weeksto score for the presence of the dicamba intolerance phenotype. Incertain embodiments, soybean plants at about the V3 vegetativedevelopment stage are exposed to an initial dicamba spray followed by asubsequent spray at V6/R1. Genotypes provided herein are especiallyuseful for providing dicamba tolerance to plants sprayed at the V6stage. As discussed herein, the vegetative stages of soybean are asfollows: VE (emergence), VC (cotyledon stage), V1 (first trifoliateleaf), V2 (second trifoliate leaf), V3 (third trifoliate leaf), V(n)(nth trifoliate leaf), and V6 (flowering will soon start). As discussedherein, the reproductive stages of soybean are as follows: R1 (beginningbloom), R2 (full bloom), R3 (beginning pod), R4 (full pod), R5(beginning seed), R6 (full seed), R7 (beginning maturity) and R8 (fullmaturity). A description of the soybean vegetative and reproductivestages can be found on the world wide web (interne) atag.ndsu.edu/pubs/plantsci/rowcrops/a1174/a1174w.htm (North Dakota StateUniversity publication A-1174, June 1999, Reviewed and Reprinted August2004).

A rating scale that evaluates the degree of dicamba intolerance can alsobe employed to identify “dicamba intolerant” and “dicamba tolerant”plants. An exemplary and non-limiting scale for evaluating the Dicambaintolerance phenotype is as follows, where a low number corresponds to a“dicamba tolerance” phenotype and the a high number correlates to a“dicamba intolerance” phenotype:

A rating of 1: Less than 10% of plants show malformationA rating of 2: 10-50% of plants show malformationA rating of 3: Greater than 50% of plants show malformation

Identification of Plants Exhibiting Reproductive Tolerance to GlyphosatePhenotype

To observe the presence or absence of reproductive tolerance toglyphosate phenotypes, transgenic soybean plants comprising a transgenethat confers glyphosate resistance are typically exposed in mid- tolate-vegetative growth stages to one or more high doses of glyphosate.Doses of glyphosate that can elicit a reproductive sensitivity phenotypeare usually at least about twice the typical application rates ofcommercial glyphosate formulations that are used to provide weed controlin transgenic, glyphosate resistant soybean plants. In terms of acidequivalents of glyphosate acid applied, typical doses of glyphosate thatcan elicit a reproductive sensitivity phenotype can range from anapplication rate of about 1.0 pounds of acid equivalent per acre (about1.12 kilograms per hectare) of glyphosate acid to about 2.25 pounds ofacid equivalent per acre (i.e. about 2.52 kilograms per hectare) ofglyphosate acid when the indicated amounts of glyphosate acid areprovided in either a commercially available glyphosate formulation orwhen the indicated amounts of glyphosate acid is provided in a similarformulation suitable for application to glyphosate-tolerant crops.Commercially available glyphosate formulations that can be used include,but are not limited to, Roundup Original MAX®, Roundup PowerMAX®,Roundup UltraMax®, or RoundUp WeatherMAX® (Monsanto Co., St. Louis, Mo.,USA); Touchdown IQ® or Touchdown Total® (Syngenta, Wilmington, Del.,USA); Glyphomax®, Glyphomax Plus®, or Glyphomax XRT® (Dow AgrosciencesLLC, Indianapolis, Ind., USA). In certain embodiments, the commerciallyavailable glyphosate formulation used is RoundUp WeatherMAX®. In certainembodiments, doses of glyphosate that can elicit a reproductivesensitivity phenotype can range from about a 2 fold application rate ofabout 42.6 ounces per acre RoundUp WeatherMax® (1.68 kilograms perhectare) to about a three fold application rate of about 63.9 ounces peracre RoundUp WeatherMax® (i.e. about 2.52 kilograms per hectare).

The reproductive sensitivity phenotype can be observed at an appropriatestage of reproductive development after herbicide application in certainsoybean varieties comprising the transgene that confers glyphosateresistance. Glyphosate is typically applied during vegetative growthstages, where applications in later vegetative growth stages cantypically elicit reproductive sensitivity at lower application rates. Incertain embodiments of these methods, glyphosate can be applied inweekly intervals (i.e. once a week) for any of 2, 3, 4 or moresuccessive weeks to score for the presence of the reproductivesensitivity phenotype. In certain embodiments, soybean plants at aboutthe V3 vegetative development stage are exposed to an initial glyphosatespray followed by a subsequent spray at the V6 vegetative stage. Incertain embodiments, soybean plants at about the V6 vegetativedevelopment stage are exposed to a glyphosate spray. As discussedherein, the vegetative stages of soybean are as follows: VE (emergence),VC (cotyledon stage), V1 (first trifoliolate leaf), V2 (secondtrifoliolate leaf), V3 (third trifoliolate leaf), V(n) (nth trifoliolateleaf), and V6 (flowering will soon start). As discussed herein, thereproductive stages of soybean are as follows R1 (beginning bloom, firstflower); R2 (full bloom, flower in top 2 nodes); R3 (beginning pod,3/16″ pod in top 4 nodes); R4 (full pod, ¾″ pod in top 4 nodes); R5 (⅛″seed in top 4 nodes); R6 (full size seed in top 4 nodes); R7 (beginningmaturity, one mature pod); and, R8 (full maturity, 95% of pods on theplant are mature). A description of the soybean vegetative andreproductive stages can be found on the world wide web (internet) atag.ndsu.edu/pubs/plantsci/rowcrops/a1174/a1174w.htm (North Dakota StateUniversity publication A-1174, June 1999, Reviewed and Reprinted August2004). Expression of the reproductive sensitivity trait can also beinfluenced by temperature, where the trait in varieties that display thereproductive sensitivity phenotype is more pronounced followingtreatment at temperatures of about 32 degrees Celsius or more.

A rating scale that evaluates the degree of reproductive sensitivity canalso be employed to identify “tolerant” and “sensitive” plants. Anexemplary and non limiting scale for evaluating the reproductivesensitivity phenotype is as follows, where the low numbers correspond toa “glyphosate reproductive tolerance” phenotype and the high numberscorrelate to a “glyphosate reproductive sensitivity” phenotype wheresterility is monitored as follows:

-   -   A rating scale of 1: Less than 10% of plants show sterility        (glyphosate reproductive tolerance)    -   A rating scale of 2: Less than 10-50% of plants show sterility    -   A rating scale 3: Greater than 50% of plants show sterility        (glyphosate reproductive sensitivity)        Soybean plant sterility can be measured by a variety of methods        that include, but are not limited to, determining pollen counts,        seed yield per plant, seed yield per pod, and the like. Controls        used to determine glyphosate reproductive sensitivity or        tolerance of a given transgenic soybean test plant comprising a        transgenic insertion event that confers glyphosate resistance in        a certain genetic background (i.e. genotype) in comparison tests        include, but are not limited to, (a) co-cultivated soybean        plants comprising the same transgenic insertion event in a        genetic background that provides for glyphosate reproductive        sensitivity; and/or (b) co-cultivated soybean plants comprising        the same transgenic insertion event in a genetic background that        provides for glyphosate reproductive tolerance, where the test        and control plants are sprayed with glyphosate. Additional        controls used to determine glyphosate reproductive sensitivity        or tolerance can also include, but are not limited to,        co-cultivated soybean plants of the same genotypes (i.e soybean        plants that are isogenic with respect to both the transgenic        insertion event and genetic background as either the test or        control soybean lines) that are not sprayed with glyphosate.        Introgression of a Genomic Region Associated with a Dicamba        Tolerance Phenotype

Also provided herewith is unique soybean germplasm comprising anintrogressed genomic region that is associated with a dicamba tolerancephenotype and methods of obtaining the same. Marker-assistedintrogression involves the transfer of a chromosomal region, defined byone or more markers, from one germplasm to a second germplasm. Offspringof a cross that contain the introgressed genomic region can beidentified by the combination of markers characteristic of the desiredintrogressed genomic region from a first germplasm (i.e. such as adicamba tolerance germplasm) and both linked and unlinked markerscharacteristic of the desired genetic background of a second germplasm(i.e. a dicamba intolerance germplasm). In addition to the markersprovided herewith that identify alleles of genomic region that isassociated with a dicamba tolerance phenotype, flanking markers thatfall on both the telomere proximal end of the genomic region on linkagegroup L (chromosome 19) and the centromere proximal end of the linkagegroup L (chromosome 19) genomic region are also provided in Tables 1 and2. Table 2 is provided at the end of the specification immediatelybefore the claims. Such flanking markers are useful in a variety ofbreeding efforts that include, but are not limited to, introgression ofthe genomic region associated with a dicamba tolerance phenotype into agenetic background comprising markers associated with germplasm thatordinarily contains the allelic forms of the genomic region that isassociated with a “Dicamba intolerance” phenotype. Telomere proximalflanking markers that can be used in these methods include, but are notlimited to, asmbl_(—)11856 (SEQ ID NO: 1), TC122822 (SEQ ID NO: 2),BI967232 (SEQ ID NO: 3), and/or polymorphisms in any of the loci listedin Table 2 of the Specification located between starting base 16426 (thetelomere proximal base) of locus asmbl_(—)11856 and starting base 92334of locus M0205928 (SEQ ID NO: 4). Centromere proximal flanking markersthat can be used in these methods include, but are not limited to,M0205537 (SEQ ID NO: 15), M0202715 (SEQ ID NO: 16), M0206286 (SEQ ID NO:17), M0206054 (SEQ ID NO: 18) and M0205375 (SEQ ID NO: 19) and/orpolymorphisms in any of the other loci listed in Table 2 that arecentromere proximal to BU765955 (SEQ ID NO: 12). Soybean plants whereinthe two subregions that are respectively flanked by loci M0205928 (SEQID NO: 4) and M0129138 (SEQ ID NO: 6 and by loci BU551363 (SEQ ID NO: 9)and BU765955 (SEQ ID NO: 12) are selectively introgressed can beobtained by using the BU551345 (SEQ ID NO: 7), SATT723, and/or M0114388(SEQ ID NO: 8) markers, or by using any of the markers located betweenthese two subregions that are provided in Table 2. Any of theaforementioned polymorphisms can be identified by sequencing loci fromdicamba intolerant and dicamba tolerance germplasms. Additional markerslocated on linkage group L (chromosome 19) and other chromosomes aredisclosed in US Patent Application Publication 20090208964. Publiclyavailable marker databases from which additional useful markers locatedon linkage group L (chromosome 19) and other chromosomes can be obtainedinclude, but are not limited to, the soybase.org website on the internetthat is administered by the United States Agricultural Research Service,the United States Department of Agriculture, and Iowa State University.Soybean plants or germplasm comprising an introgressed genomic regionthat is associated with a dicamba tolerance phenotype wherein at least10%, 25%, 50%, 75%, 90%, or 99% of the remain genomic sequences carrymarkers characteristic of soybean plants or germplasm that are otherwiseor ordinarily comprise a genomic region associated with the Dicambaintolerance phenotype are thus provided.

Soybean Plants Comprising Genomic Region Associated with the DicambaIntolerance and Dicamba Tolerance Phenotypes and Transgenes that ConferResistance to Dicamba

A non-limiting and exemplary list of soybean plants that comprisegenomic regions associated with either a dicamba-intolerance or adicamba tolerance phenotype are provided herewith in Table 3.

TABLE 3 Soybean varieties comprising a genomic region associated with adicamba tolerance or dicamba intolerant phenotype. ATCC VarietyDepository Date of Branded Dicamba US Patent Name in Accession PatentName ¹ Phenotype Number Patent Number ² Issue AG3102 Intolerant7,964,777 7629164 PTA-10825 Jun. 21, 2011 AG3603 Intolerant 7,592,516D4328762 PTA-9797 Sep. 22, 2009 AG4903 AG4907 Intolerant 7,687,685D5703684 PTA-10153 Mar. 30, 2010 AG0803 Tolerant 7,498,489 4498438PTA-9064 AG3102 Tolerant 7,964,777 7629164 PTA-10825 Jun. 21, 2011AG3603 Tolerant 7,592,516 D4328762 PTA-9797 Sep. 22, 2009 BBL3606N0RBL3307M2- D0RL AG4903 AG4907 Tolerant 7,687,685 D5703684 PTA-10153 Mar.30, 2010 260744-14 AFL0506C0R Tolerant 7,723,583 D5864369 PTA-10719 May25, 2010 AG0808 Tolerant 7,732,672 D5142326 PTA-10168 Jun. 8, 2010263619-24 4065735-51 5463213-25 AG1002 Tolerant 7,294,770 5826175PTA-8148 Nov. 13, 2007 AG1403 Tolerant 7,557,273 6943322 PTA-9554 Jul.7, 2009 AG1406 Tolerant 7,732,673 D5232589 PTA-10268 Jun. 8, 2010CSR1920 Tolerant 7,728,199 7821295 PTA-10519 Jun. 1, 2010 15733-79-595081541-27 5464705-06 AG2110 Tolerant 7,678,965 D5624834 PTA-10134 Mar.16, 2010 AG2606 Tolerant 7,622,644 D4201139 PTA-9749 Nov. 24, 2009AG2909 Tolerant 7,999,153 D5502014 PTA-11081 Aug. 16, 2011 AG2921VTolerant 7,390,940 4858197 PTA-9072 Jun. 24, 2008 AG3021V Tolerant7,572,958 D4361423 PTA-9801 Aug. 11, 2009 BOX2906H0R DFN3306B0R Tolerant7,626,089 D4311702 PTA-9781 Dec. 1, 2009 CSRS4782N Tolerant 7,700,847D5898941 PTA-10598 Apr. 20, 2010 GL4807A2- Tolerant 7,868,230 D5523145PTA-11362 Jan. 11, 2011 D0RN ¹ Branded names of Asgrow ® (designated“AG”) and DEKALB ® soybean varieties from Monsanto Co. 800 N. LindberghBlvd., St. Louis, MO, USA. ² Deposit numbers of seed available throughthe American Type Culture Collection (ATCC), 10801 University Blvd.,Manassas, Va., USA, 20110-2209. ³ Dicamba phenotype is the phenotypeobserved in the indicated germplasm containing a transgene that confersresistance to dicamba when exposed to dicamba.

Also provided herewith are additional soybean plants that comprising agenomic region associated with a dicamba intolerant or dicamba tolerancephenotype that are identified by use of the markers provided in Table 1and/or Table 2 and/or methods provided herein. Any of the soybean plantsidentified in Table 3 or other soybean plants that are otherwiseidentified using the markers or methods provided herein can be used inmethods that include, but are not limited to, methods of obtainingsoybean plants with an introgressed dicamba tolerance locus, obtaining asoybean plant that exhibits a dicamba tolerance phenotype, or obtaininga soybean plant comprising in its genome a genetic region associatedwith a dicamba tolerance phenotype.

In certain embodiments, the soybean plants provided herein or used inthe methods provided herein can comprise a transgene that confersresistance to dicamba. In certain embodiments, the dicamba tolerantsoybean plants can comprise a transgene encoding a dicamba-degradingdicamba monoxygenase (DMO) enzyme that catalyzes the conversion ofherbicidal dicamba (3,6-dichloro-o-anisic acid) to a non-toxic3,6-dichlorosalicylic acid. In certain embodiments, thedicamba-degrading dicamba monoxygenase (DMOw) comprise a DMO enzymedisclosed in U.S. Pat. Nos. 7,022,896, 7,105,724, and 7,812,224, eachincorporated herein by reference in their entireties. Exemplary andnon-limiting DMOw dicamba monooxygenase encoding nucleic acid andprotein sequences are provided herewith as SEQ ID NO: 20 and SEQ ID NO:21. In certain embodiments, the dicamba tolerant soybean plants cancomprise a dicamba monoxygenase variant which exhibits improvedcatalytic parameters such as increased turnover number and/or a lower kmfor the substrate, improved catalysis at lower pH values, and/orimproved catalysis at higher temperatures relative to an unaltereddicamba monooxygenase. In certain embodiments, the dicamba monoxygenasevariant comprises a DMOc variant enzyme disclosed in U.S. Pat. No.7,884,262, incorporated herein by reference in its entirety. Exemplaryand non-limiting DMOc dicamba monooxygenase variant encoding nucleicacid and protein sequences are provided herewith as SEQ ID NO: 22 andSEQ ID NO: 23. In certain embodiments, a dicamba monooxygenase isoperably linked to a chloroplast transit peptide (CTP). Operable linkageof certain CTPs to DMO is disclosed in U.S. Pat. No. 8,084,666, which isincorporated herein by reference in its entirety. In certainembodiments, it is contemplated that the soybean plants used herein cancomprise one or more specific genomic insertion(s) of a dicamba toleranttransgene including, but not limited to, as those found in MON87708soybean (deposited under ATCC accession number PTA-9670 and described inUS Patent Application Publication Number 20110067134).

In certain embodiments, the soybean plants provided herein or used inthe methods provided herein can comprise a transgene that conferstolerance to glyphosate. Transgenes that can confer tolerance toglyphosate include, but are not limited to, transgenes that encodeglyphosate tolerant Class I EPSPS (5-enolpyruvylshikimate-3-phosphatesynthases) enzymes or glyphosate tolerant Class II EPSPS(5-enolpyruvylshikimate-3-phosphate synthases) enzymes. Usefulglyphosate tolerant EPSPS enzymes provided herein are disclosed in U.S.Pat. Nos. 6,803,501, RE39,247, 6,225,114, 5,188,642, and 4,971,908. Incertain embodiments, the glyphosate tolerant soybean plants can comprisea transgene encoding a glyphosate oxidoreductase or other enzyme whichdegrades glyphosate. Glyphosate oxidoreductase enzymes had beendescribed in U.S. Pat. No. 5,776,760 and U.S. Reissue Pat. RE38,825. Incertain embodiments the soybean plant can comprise a transgene encodinga glyphosate N-acetyltransferase gene that confers tolerance toglyphosate. In certain embodiments, the soybean plant can comprise aglyphosate n-acetyltransferase encoding transgene such as thosedescribed in U.S. Pat. No. 7,666,644. In still other embodiments,soybean plants comprising combinations of transgenes that conferglyphosate tolerance are provided. Soybean plants comprising both aglyphosate resistant EPSPS and a glyphosate N-acetyltransferase are alsoprovided herewith. In certain embodiments, it is contemplated that thesoybean plants used herein can comprise one or more specific genomicinsertion(s) of a glyphosate tolerant transgene including, but notlimited to, as those found in: i) MON89788 soybean (deposited under ATCCaccession number PTA-6708 and described in US Patent ApplicationPublication Number 20100099859), ii) GTS 40-3-2 soybean (Padgette etal., Crop Sci. 35: 1451-1461, 1995), iii) event 3560.4.3.5 soybean (seeddeposited under ATCC accession number PTA-8287 and described in USPatent Publication 20090036308), or any combination of i (MON89788soybean), ii (GTS 40-3-2 soybean), and iii (event 3560.4.3.5 soybean).

In certain embodiments, the gene that confers resistance to dicamba is agene encoding a Dicamba monooxygenase (DMO). The DMO gene is a microbialgene that has been transformed into soybean and cotton to confertolerance to the dicamba herbicide. The DMO protein expressed in theplants transformed with the DMO gene actively metabolizes dicamba to3,6-dichloro salicylic acid (DCSA), which lacks herbicidal activity. Incertain embodiments, Dicamba resistant (DR) soybeans can be crossed with“RoundUp Ready 2 Yield™” (RR2Y) soybeans to generate a stack (RR2YxDR)which can confer resistance to both dicamba and glyphosate. It has beenobserved in certain germplasms that a herbicide traits (i.e. transgeneconferred glyphosate and dicamba resistance)×germplasm interaction canresult in increased sensitivity to dicamba (i.e. “dicamba intolerance”)that may be commercially undesirable. In certain embodiments, favorablehaplotypes are provided herein which are associated with robusttolerance to dicamba and glyphosate, and which are useful for selectionof RR2YxDR soybeans that do not exhibit dicamba intolerance.

In certain embodiments, it is contemplated that genotypic assays thatprovide for non-destructive identification of the plant or plants can beperformed either in seed, the emergence stage, the “VC” stage (i.e.cotyledons unfolded), the V1 stage (appearance of first node andunifoliate leaves), the V2 stage (appearance of the first trifoliateleaf), and thereafter. In certain embodiments, non-destructive genotypicassays are performed in seed using apparati and associated methods asdescribed in U.S. Pat. Nos. 6,959,617; 7,134,351; 7,454,989; 7,502,113;7,591,101; 7,611,842; and 7,685,768, which are incorporated herein byreference in their entireties. In certain embodiments, non-destructivegenotypic assays are performed in seed using apparati and associatedmethods as described in US Patent Application Publications 20100086963,20090215060, and 20090025288, which are incorporated herein by referencein their entireties. Published U.S. Patent Applications US 2006/0042527,US 2006/0046244, US 2006/0046264, US 2006/0048247, US 2006/0048248, US2007/0204366, and US 2007/0207485, which are incorporated herein byreference in their entirety, also disclose apparatus and systems for theautomated sampling of seeds as well as methods of sampling, testing andbulking seeds. Thus, in a certain embodiments, any of the methodsprovided herein can comprise screening for markers in individual seedsof a population wherein only seed with at least one genotype of interestis advanced.

Soybean Plants Comprising a Genomic Region Associated with StackedTransgenic Trait Improvement and Transgenes that Confer Resistance toOther Herbicides and/or Insects

In certain embodiments, soybean plants comprising a genomic regionassociated with stacked transgenic trait improvement (or the dicambatolerance phenotype) and at least one additional herbicide resistancetransgene selected from the group consisting of a dicamba resistanceconferring transgene, a 2,4-D resistance conferring transgene, and aglufosinate resistance conferring transgene and/or at least onetransgene encoding a product that confers insect resistance selectedfrom the group consisting of a dsRNA that inhibits a target gene of aninsect pest, a patatin, a Bacillus thuringiensis insecticidal protein, aXenorhabdus insecticidal protein, a Photorhabdus insecticidal protein, aBacillus laterosporous insecticidal protein, a Bacillus sphaericusinsecticidal protein, and a lignin are provided herein. Such transgenictrait improvements that can occur in plants comprising the genomicregions provided herein can be ascertained by comparing transgenic traitperformance in varieties containing the genomic regions to thetransgenic trait performance in other varieties lacking the genomicregion. Such transgenic herbicide resistance trait improvements that canoccur in plants comprising the genomic regions provided herein caninclude, but are not limited to, decreased phytotoxicity upon herbicideexposure in varieties containing the genomic regions conferring theimproved transgenic trait performance and the corresponding herbicideresistance conferring transgene in comparison to other varieties lackingthe genomic region and the corresponding herbicide resistance conferringtransgene upon herbicide exposure. Various dsRNAs that inhibit a targetgene of an insect pest are described in US Patent ApplicationPublication Number 20120137387, which is specifically incorporatedherein by reference in its entirety. A Bacillus thuringiensisinsecticidal protein can be any of a number of insecticidal proteinsincluding but not limited to a Cry1, a Cry3, a TIC851, a CryET70, aCry22, a TIC901, a TIC1201, a TIC407, a TIC417, a binary insecticidalprotein CryET33 and CryET34, a binary insecticidal protein CryET80 andCryET76, a binary insecticidal protein TIC100 and TIC101, a binaryinsecticidal protein PS149B1, a VIP insecticidal protein, a TIC900 orrelated protein, or combinations of the insecticidal proteins ET29 orET37 with insecticidal proteins TIC810 or TIC812, and insecticidalchimeras of any of the preceding insecticidal proteins. A Bacillusthuringiensis insecticidal protein can be any of a number ofinsecticidal proteins including but not limited to a Cry1Aa, Cry1Ab,Cry1Ac, Cry1Ad, Cry1Ae, Cry1Ba, Cry1Bb, Cry1Ca, Cry1Cb, Cry1Da, Cry1Db,Cry1Ea, Cry1Eb, Cry1Fa, Cry1Fb, Cry1Ga, Cry1Ha, Cry2Aa, Cry2Ab, Cry1Ja,Cry1 Ka, Cry11 Aa, Cry11Ab, Cry12Aa, Cry3Ba, Cry3Bb, Cry3C, Cry4a,Cry4Ba, Cry5a, Cry5Ab, Cry6Aa, Cry6Ba, Cry7Aa, Cry7Ab, Cry8Aa, Cry8Ba,Cry8Ca, Cry9Aa, Cry9Ba, Cry9Ca, Cry10Aa, Cry11Aa, Cry12Aa, Cry13Aa,Cry14Aa, Cry15Aa, Cyt1Aa, and Cyt2Aa protein or an insecticidal chimerasthereof. Insecticidal chimeras of certain Bacillus thuringiensisinsecticidal proteins include, but are not limited to, Cry1A/F and otherchimeras disclosed in US Patent Application Publication No. 20090143298.Such transgenic insect resistance trait improvements that can occur inplants comprising the genomic regions provided herein can include, butare not limited to, decreased insect-mediated plant damage, or increasedinsect death, inhibition, stunting, or cessation of insect feeding invarieties containing the genomic regions that confer the transgenictrait performance in comparison to other varieties lacking the genomicregion.

Molecular Assisted Breeding Techniques

Genetic markers that can be used in the practice of the instantinvention include, but are not limited to, are Restriction FragmentLength Polymorphisms (RFLP), Amplified Fragment Length Polymorphisms(AFLP), Simple Sequence Repeats (SSR), Single Nucleotide Polymorphisms(SNP), Insertion or Deletion Polymorphisms (Indels), Variable NumberTandem Repeats (VNTR), and Random Amplified Polymorphic DNA (RAPD), andothers known to those skilled in the art. Marker discovery anddevelopment in crops provides the initial framework for applications tomarker-assisted breeding activities (US Patent Applications2005/0204780, 2005/0216545, 2005/0218305, and 2006/00504538). Theresulting “genetic map” is the representation of the relative positionof characterized loci (DNA markers or any other locus for which allelescan be identified) along the chromosomes. The measure of distance onthis map is relative to the frequency of crossover events between sisterchromatids at meiosis.

As a set, polymorphic markers serve as a useful tool for fingerprintingplants to inform the degree of identity of lines or varieties (U.S. Pat.No. 6,207,367). These markers form the basis for determiningassociations with phenotype and can be used to drive genetic gain. Theimplementation of marker-assisted selection is dependent on the abilityto detect underlying genetic differences between individuals.

Certain genetic markers for use in the present invention include“dominant” or “codominant” markers. “Codominant markers” reveal thepresence of two or more alleles (two per diploid individual). “Dominantmarkers” reveal the presence of only a single allele. The presence ofthe dominant marker phenotype (e.g., a band of DNA) is an indicationthat one allele is present in either the homozygous or heterozygouscondition. The absence of the dominant marker phenotype (e.g., absenceof a DNA band) is merely evidence that “some other” undefined allele ispresent. In the case of populations where individuals are predominantlyhomozygous and loci are predominantly dimorphic, dominant and codominantmarkers can be equally valuable. As populations become more heterozygousand multiallelic, codominant markers often become more informative ofthe genotype than dominant markers.

In another embodiment, markers that include, but are not limited to,single sequence repeat markers (SSR), AFLP markers, RFLP markers, RAPDmarkers, phenotypic markers, isozyme markers, single nucleotidepolymorphisms (SNPs), insertions or deletions (Indels), single featurepolymorphisms (SFPs, for example, as described in Borevitz et al. 2003Gen. Res. 13:513-523), microarray transcription profiles, DNA-derivedsequences, and RNA-derived sequences that are genetically linked to orcorrelated with dicamba tolerance loci, regions flanking dicambatolerance loci, regions linked to dicamba tolerance loci, and/or regionsthat are unlinked to dicamba tolerance loci can be used in certainembodiments of the instant invention.

In one embodiment, nucleic acid-based analyses for determining thepresence or absence of the genetic polymorphism (i.e. for genotyping)can be used for the selection of seeds in a breeding population. A widevariety of genetic markers for the analysis of genetic polymorphisms areavailable and known to those of skill in the art. The analysis may beused to select for genes, portions of genes, QTL, alleles, or genomicregions (Genotypes) that comprise or are linked to a genetic marker thatis linked to or correlated with dicamba tolerance loci, regions flankingdicamba tolerance loci, regions linked to dicamba tolerance loci, and/orregions that are unlinked to dicamba tolerance loci can be used incertain embodiments of the instant invention.

Nucleic acid analysis methods provided herein include, but are notlimited to, PCR-based detection methods (for example, TaqMan™ assays),microarray methods, mass spectrometry-based methods and/or nucleic acidsequencing methods. In one embodiment, the detection of polymorphicsites in a sample of DNA, RNA, or cDNA may be facilitated through theuse of nucleic acid amplification methods. Such methods specificallyincrease the concentration of polynucleotides that span the polymorphicsite, or include that site and sequences located either distal orproximal to it. Such amplified molecules can be readily detected by gelelectrophoresis, fluorescence detection methods, or other means.

A method of achieving such amplification employs the polymerase chainreaction (PCR) (Mullis et al. 1986 Cold Spring Harbor Symp. Quant. Biol.51:263-273; European Patent 50,424; European Patent 84,796; EuropeanPatent 258,017; European Patent 237,362; European Patent 201,184; U.S.Pat. No. 4,683,202; U.S. Pat. No. 4,582,788; and U.S. Pat. No.4,683,194), using primer pairs that are capable of hybridizing to theproximal sequences that define a polymorphism in its double-strandedform.

Methods for typing DNA based on mass spectrometry can also be used. Suchmethods are disclosed in U.S. Pat. Nos. 6,613,509 and 6,503,710, andreferences found therein. Polymorphisms in DNA sequences can be detectedor typed by a variety of effective methods well known in the artincluding, but not limited to, those disclosed in U.S. Pat. Nos.5,468,613, 5,217,863; 5,210,015; 5,876,930; 6,030,787; 6,004,744;6,013,431; 5,595,890; 5,762,876; 5,945,283; 5,468,613; 6,090,558;5,800,944; 5,616,464; 7,312,039; 7,238,476; 7,297,485; 7,282,355;7,270,981 and 7,250,252 all of which are incorporated herein byreference in their entireties. However, the compositions and methods ofthe present invention can be used in conjunction with any polymorphismtyping method to type polymorphisms in genomic DNA samples. Thesegenomic DNA samples used include but are not limited to genomic DNAisolated directly from a plant, cloned genomic DNA, or amplified genomicDNA.

For instance, polymorphisms in DNA sequences can be detected byhybridization to allele-specific oligonucleotide (ASO) probes asdisclosed in U.S. Pat. Nos. 5,468,613 and 5,217,863. U.S. Pat. No.5,468,613 discloses allele specific oligonucleotide hybridizations wheresingle or multiple nucleotide variations in nucleic acid sequence can bedetected in nucleic acids by a process in which the sequence containingthe nucleotide variation is amplified, spotted on a membrane and treatedwith a labeled sequence-specific oligonucleotide probe.

Target nucleic acid sequence can also be detected by probe ligationmethods as disclosed in U.S. Pat. No. 5,800,944 where sequence ofinterest is amplified and hybridized to probes followed by ligation todetect a labeled part of the probe.

Microarrays can also be used for polymorphism detection, whereinoligonucleotide probe sets are assembled in an overlapping fashion torepresent a single sequence such that a difference in the targetsequence at one point would result in partial probe hybridization(Borevitz et al., Genome Res. 13:513-523 (2003); Cui et al.,Bioinformatics 21:3852-3858 (2005). On any one microarray, it isexpected there will be a plurality of target sequences, which mayrepresent genes and/or noncoding regions wherein each target sequence isrepresented by a series of overlapping oligonucleotides, rather than bya single probe. This platform provides for high throughput screening aplurality of polymorphisms. A single-feature polymorphism (SFP) is apolymorphism detected by a single probe in an oligonucleotide array,wherein a feature is a probe in the array. Typing of target sequences bymicroarray-based methods is disclosed in U.S. Pat. Nos. 6,799,122;6,913,879; and 6,996,476.

Target nucleic acid sequence can also be detected by probe linkingmethods as disclosed in U.S. Pat. No. 5,616,464, employing at least onepair of probes having sequences homologous to adjacent portions of thetarget nucleic acid sequence and having side chains which non-covalentlybind to form a stem upon base pairing of the probes to the targetnucleic acid sequence. At least one of the side chains has aphotoactivatable group which can form a covalent cross-link with theother side chain member of the stem.

Other methods for detecting SNPs and Indels include single baseextension (SBE) methods. Examples of SBE methods include, but are notlimited, to those disclosed in U.S. Pat. Nos. 6,004,744; 6,013,431;5,595,890; 5,762,876; and 5,945,283. SBE methods are based on extensionof a nucleotide primer that is adjacent to a polymorphism to incorporatea detectable nucleotide residue upon extension of the primer. In certainembodiments, the SBE method uses three synthetic oligonucleotides. Twoof the oligonucleotides serve as PCR primers and are complementary tosequence of the locus of genomic DNA which flanks a region containingthe polymorphism to be assayed. Following amplification of the region ofthe genome containing the polymorphism, the PCR product is mixed withthe third oligonucleotide (called an extension primer) which is designedto hybridize to the amplified DNA adjacent to the polymorphism in thepresence of DNA polymerase and two differentially labeleddideoxynucleosidetriphosphates. If the polymorphism is present on thetemplate, one of the labeled dideoxynucleosidetriphosphates can be addedto the primer in a single base chain extension. The allele present isthen inferred by determining which of the two differential labels wasadded to the extension primer. Homozygous samples will result in onlyone of the two labeled bases being incorporated and thus only one of thetwo labels will be detected. Heterozygous samples have both allelespresent, and will thus direct incorporation of both labels (intodifferent molecules of the extension primer) and thus both labels willbe detected.

In another method for detecting polymorphisms, SNPs and Indels can bedetected by methods disclosed in U.S. Pat. Nos. 5,210,015; 5,876,930;and 6,030,787 in which an oligonucleotide probe having a 5′ fluorescentreporter dye and a 3′ quencher dye covalently linked to the 5′ and 3′ends of the probe. When the probe is intact, the proximity of thereporter dye to the quencher dye results in the suppression of thereporter dye fluorescence, e.g. by Forster-type energy transfer. DuringPCR forward and reverse primers hybridize to a specific sequence of thetarget DNA flanking a polymorphism while the hybridization probehybridizes to polymorphism-containing sequence within the amplified PCRproduct. In the subsequent PCR cycle DNA polymerase with 5′→3′exonuclease activity cleaves the probe and separates the reporter dyefrom the quencher dye resulting in increased fluorescence of thereporter.

In another embodiment, the locus or loci of interest can be directlysequenced using nucleic acid sequencing technologies. Methods fornucleic acid sequencing are known in the art and include technologiesprovided by 454 Life Sciences (Branford, Conn.), Agencourt Bioscience(Beverly, Mass.), Applied Biosystems (Foster City, Calif.), LI-CORBiosciences (Lincoln, Nebr.), NimbleGen Systems (Madison, Wis.),Illumina (San Diego, Calif.), and VisiGen Biotechnologies (Houston,Tex.). Such nucleic acid sequencing technologies comprise formats suchas parallel bead arrays, sequencing by ligation, capillaryelectrophoresis, electronic microchips, “biochips,” microarrays,parallel microchips, and single-molecule arrays, as reviewed by R.F.Service Science 2006 311:1544-1546.

The markers to be used in the methods of the present invention shouldpreferably be diagnostic of origin in order for inferences to be madeabout subsequent populations. Experience to date suggests that SNPmarkers may be ideal for mapping because the likelihood that aparticular SNP allele is derived from independent origins in the extantpopulations of a particular species is very low. As such, SNP markersappear to be useful for tracking and assisting introgression of QTLs,particularly in the case of Genotypes.

EXAMPLES

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples which follow representtechniques discovered by the inventor to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Example 1

Marker-assisted backcrossing (MABC) is a common breeding methodology totransfer a gene of interest into a desired recurrent parent. MABC wasused to transfer both the dicamba resistance (DMO) transgene (U.S.Patent Appl. US20110067134) and the glyphosate resistant RoundUp Ready 2Yield™ (RR2Y) CP4 genes (U.S. Pat. No. 7,632,985) into several recurrentparents. The process involved making three backcrosses to the recurrentparent and using genome wide markers to target the recovery of 95% orgreater of the recurrent parent genome. In this process, markers wereused to confirm the presence of the DMO and RR2Y CP4 genes and theabsence of the RR1 CP4 gene. The haplotype at the dicamba tolerancelocus for each recurrent parent was known.

Observations on MABC lines whose recurrent parents contained differenthaplotypes were made. For each MABC, there were several variants, witheach variant tracing to a unique BC3F1 plant. The MABC lines were grownin spray trials at two locations throughout the United States with tworeplications at each location. Each line was planted in a paired, twelvefoot plot. Each plot was sprayed at V3 with 0.75 lb a.e./acre ofglyphosate and 1.0 lb a.e./acre dicamba followed by the same treatmentat V6. Malformation was measured as the percentage of plants within aplot that were malformed. For each MABC, the data were averaged acrossvariants, replications, and locations to place into one the followingcategories:

1. No malformation: No severe malformation detected

2. Malformation: >20% severe malformation

The data are presented in Table 4. The 6 MABC lines with a CCAATT orTTAATT haplotype all showed malformation whereas the 25 lines with theTTTTCC haplotype showed no malformation. These observations indicatedthat the presence of certain haplotypes at the dicamba tolerance locusin lines containing the DMO and RR2Y CP4 transgenes leads tomalformation following dicamba treatment.

TABLE 4 Recurrent Parent Haplotypes and Malformation Phenotypes inResponse to Dicamba Application. Recurrent Number of M Response ParentObservations G M0101742 M0205350 M0102027 to Dicamba AG3102 24 3 CC AATT Malformation AG3603 30 3 CC AA TT Malformation BBL3606 30 3 CC AA TTMalformation N0R BL3307M 30 3 CC AA TT Malformation 2-D0RL AG4903 36 4TT AA TT Malformation AG4907 36 4 CC AA TT Malformation 260744-14 24 0TT TT CC No Malformation AFL0506 24 0 TT TT CC No Malformation C0RAG0803 24 0 TT TT CC No Malformation AG0808 24 0 TT TT CCNo Malformation 263619-24 24 1 TT TT CC No Malformation 4065735-51 24 1TT TT CC No Malformation 5463213-25 36 1 TT TT CC No Malformation AG100224 1 TT TT CC No Malformation AG1403 24 1 TT TT CC No MalformationAG1406 24 1 TT TT CC No Malformation CSR1920 36 1 TT TT CCNo Malformation 15733-79-59 30 2 TT TT CC No Malformation 5081541-27 122 TT TT CC No Malformation 5464705-06 30 2 TT TT CC No MalformationAG2110 36 2 TT TT CC No Malformation AG2606 29 2 TT TT CCNo Malformation AG2909 30 2 TT TT CC No Malformation AG2921V 30 2 TT TTCC No Malformation AG3021V 30 3 TT TT CC No Malformation AG3803 30 3 TTTT CC No Malformation BOX2906 30 3 TT TT CC No Malformation H0R AG380330 3 TT TT CC No Malformation DFN3306 24 3 TT TT CC No Malformation B0RCSRS478 36 4 TT TT CC No Malformation 2N GL4807A 36 4 TT TT CCNo Malformation 2-D0RN

Example 2 Haplotypes Associated with a Malformation and SterilityPhenotypes for MG 6 and 7 BC2F3:4 Populations Upon Herbicide Application

The effect of different haplotypes on response to dicamba and glyphosatewere evaluated by comparing MG6-7 BC2F3:4 lines that contained a CP4transgene that confers tolerance to glyphosate and a DMO transgene thatconfers tolerance to dicamba. The recurrent parent of the population wasRP1 that had the CCAACC haplotype for markers NS0101742, NS0205350, andNS0102027 markers, respectively. The donor parent of the population wasDP1 that had a TTTTCC haplotype. During the breeding process, thehaplotype for each line at the dicamba tolerance locus was not known.Markers were used to select for the absence of the RR1 CP4 gene, and forthe presence of the RR2Y CP4 gene and the Dicamba resistance DMO gene.Table 5 describes the breeding history for this material.

TABLE 5 Breeding History for Plant Material in Example 2. Gen. SeasonYear Location Breeding Activity Cross Winter 2007 Isabella, Puerto RicoCross F1 Summer 2008 Isabella, Puerto Rico Backcross BC1F1 Winter 2008Isabella, Puerto Rico Backcross BC2F1 Summer 2009 Isabella, Puerto RicoBulk BC2F2 Winter 2009 Isabella, Puerto Rico Bulk BC2F3 Summer 2010Mount Olive, NC Single plant selection BC2F4 Summer 2011 Mount Olive, NCProgeny row

A total of 360 BC2F3:4 lines were grown in Mount Olive, N.C. in 2011.The lines were grown in a single four foot rows with one replication.The lines were sprayed with 0.75 lb a.e./acre of glyphosate at V3 plantstage followed by the same rate of glyphosate at V6 plant stage plus 0.5lb a.e./acre of dicamba.

Rating Scales: Malformation:

A rating of 1: Less than 10% of plants show malformationA rating of 2: 10-50% of plants show malformationA rating of 3: Greater than 50% of plants show malformation

Sterility:

A rating of 1: Less than 10% of plants show sterilityA rating of 2: 10-50% of plants show sterilityA rating of 3: Greater than 50% of plants show sterility

Table 6 shows the distribution of lines across the different ratingclasses.

TABLE 6 Malformation and Sterility Ratings for Soybean Populations.Malformation Rating 1 2 3 Sterility Rating Number of lines per ratingclass 1 154 18 3 2 58 61 52 3 2 2 10

The 51 lines that were rated “1” for malformation and “1” for sterilityand the 62 lines that were rated “3” for malformation and “2” or “3” forsterility were genotyped for the three dicamba tolerance markers asshown in Table 7.

TABLE 7Haplotypes Associated with a Malformation and Sterility Ratings for51 Soybean Lines. Marker Haplotype Rating Line Number M0101742 M0205350M0102027 Malformation Sterility 123 TT TT CC 1 1 124 CC AA CC 3 2 126 CCAA CC 3 2 128 TT TT CC 1 1 135 TT TT CC 1 1 136 CC AA CC 3 3 140 CC AACC 3 2 141 TT TT CC 1 1 143 TT TT CC 1 1 144 CC AA CC 3 2 145 CC AA CC 32 149 CT AT CC 1 1 151 CC AA CC 3 2 154 CC AA CC 3 2 156 TT TT CC 1 1157 CT AT CC 1 1 159 CC AA CC 3 2 160 CC AA CC 3 2 164 TT TT CC 1 1 171CT AT CC 1 1 173 CC AA CC 3 2 184 CC AA CC 3 2 189 CC AA CC 3 2 193 CCAA CC 3 2 200 TT TT CC 1 1 201 CC AA CC 3 2 203 CC AA CC 3 2 204 CT ATCC 1 1 212 CC AA CC 3 2 213 TT TT CC 1 1 214 TT TT CC 1 1 216 CC AA CC 32 217 TT TT CC 1 1 218 TT TT CC 1 1 222 CT AT CC 3 2 223 CC AA CC 3 2225 CT AT CC 1 1 228 TT TT CC 1 1 230 TT TT CC 1 1 234 CC AA CC 3 2 235TT TT CC 1 1 243 CC AA CC 3 2 246 CC AA CC 1 1 251 CC AA CC 3 3 260 CCAA CC 3 3 261 CT AT CC 1 1 262 CT AT CC 3 3 264 CT AT CC 1 1 268 TT TTCC 1 1 274 CC AA CC 3 2 277 CC AA CC 3 2 280 CC AA CC 3 2 281 CC AA CC 32 290 CC AA CC 3 2 309 CC AA CC 1 1 314 CC AA CC 3 2 316 TT TT CC 1 1317 CC AA CC 3 2 318 TT TT CC 1 1 319 TT TT CC 1 1 324 TT TT CC 1 1 329CC AA CC 3 3 330 CC AA CC 1 1 331 CC AA CC 1 1 333 CC AA CC 3 2 334 CCAA CC 1 1 336 CC AA CC 3 2 337 CC AA CC 1 1 338 TT TT CC 1 1 340 CC AACC 3 2 347 TT TT CC 1 1 348 TT TT CC 1 1 350 CT AT CC 3 2 352 CC AA CC 32 353 TT TT CC 1 1 362 CC AA CC 3 2 379 TT TT CC 1 1 380 TT TT CC 1 1381 CC AA CC 3 2 382 CT AT CC 1 1 384 CC AA CC 3 2 385 CC AA CC 3 2 393CT AT CC 1 1 396 TT TT CC 1 1 398 CC AA CC 3 2 399 CC AA CC 3 2 400 CCAA CC 3 2 408 CC AA CC 3 2 409 CC AA CC 3 2 411 TT TT CC 1 1 412 CC AACC 3 2 417 TT TT CC 1 1 421 CC AA CC 3 2 433 CT AT CC 1 1 434 TT TT CC 11 435 TT TT CC 1 1 440 CC AA CC 3 2 446 CC AA CC 3 3 449 CC AA CC 3 3452 TT TT CC 1 1 457 CC AA CC 3 3 460 CC AA CC 3 2 467 TT TT CC 1 1 468CC AA CC 3 3 470 CC AA CC 3 2 488 CC AA CC 3 2 490 CC AA CC 3 2 494 CCAA CC 3 3 495 CC AA CC 3 2 500 CC AA CC 3 2 505 CC AA CC 3 2 510 TT TTCC 1 1 512 CC AA CC 1 1

The 34 lines with the TTTTCC haplotype had a rating of “1” formalformation and “1” for sterility as summarized in Table 8.

TABLE 8 Summary of Table 7. Rating Marker Haplotype No. of linesMalformation Sterility M0101742 M0205350 M0102027 34 1 1 TT TT CC 59 32 or 3 CC AA CC  7 1 1 10 1 1 CT AT CC  3 3 2 or 3

Out of the 66 lines with the CCAACC haplotype, 59 had a rating of “3”for malformation and a rating of “2” or “3” for sterility. The 13 linesheterozygous for the markers had a range of ratings for malformation andsterility.

These results support the observations that certain haplotypes at thedicamba tolerance locus in lines containing the RR2Y CP4 and DMOtransgenes causes sterility from glyphosate and malformation fromdicamba applications made at the V6 plant stage

Example 3 Haplotypes Associated with a Malformation and SterilityPhenotypes for MG 3 and 4 Populations Upon Herbicide Application inFontezuela, Argentina

The effect of different haplotypes on response to glyphosate wereevaluated by measuring observing sterility in MG3 to MG4 lines inglyphosate spray trials in Fontezuela, Argentina in 2012. The lines werefrom populations known to segregate for markers at the dicamba tolerancelocus based on parental haplotypes. During the breeding process, thehaplotype for each line at the dicamba tolerance locus was not known.Table 9 describes the breeding history for this material.

TABLE 9 Breeding History for Plant Material in Example 3. Gen. SeasonYear Location Breeding Activity Cross Winter or 2010 Isabella, PuertoRico, Cross Summer or Galena, MD F1 Summer or 2010 Isabella, Puerto RicoBulk Winter F2 Winter 2011 Kunia, HI Bulk F3 Summer 2011 Stonington, ILSingle plant selection F4 Summer 2012 Fontezuela, Argentina Progeny row

Markers were used to select for the absence of the RR1 CP4 gene, and forthe presence of the RR2Y CP4 gene and the Dicamba resistance (DMO) gene.A total of 1,083 F3:4 lines across six populations were planted in 4foot single row plots. Remnant seed from each line was used forgenotyping the lines across two markers at the dicamba tolerance locus.The lines were sprayed with 1.125 lb a.e./acre of glyphosate at V3 plantstage followed by the same rate applied at V6. Sterility ratings weretaken at maturity.

A rating of 1: Less than 10% of plants show sterilityA rating of 2: 10-50% of plants show sterilityA rating of 3: Greater than 50% of plants show sterility

The sterility ratings by haplotype class are shown in Table 10.

TABLE 10 Haplotypes Associated with sterility ratingsfor Selected Soybean Populations. No. lines Marker Haplotype Totalper rating class Population M0101742 M0205350 No. of Lines 1 2 3 POP1 TTTT 42 42 CC AA 27 10 17 CT AT 25  1 23  1 POP2 TT TT 83 83 TT AA 23  815 TT AT 36 11 25 POP3 TT TT 81 81 CC AA 89 24 65 CT AT 40  4 27  9 POP4TT TT 69 69 CC AA 43  1  2 40 CT AT 39  1 27 11 TT TT 75 75 TT AA 62  359 TT AT 44 44 POP5 TT TT 185  185  CC AA 66  2 64 CT AT 54  4 47  3Across populations TT TT 535  535   0  0 (POP1-5) CC AA 225   1 38 186 TT AA 85  0 11 74 CT AT 158  10 124  24 TT AT 80  0 55 25

Lines with the TTTT haplotype for markers M0101742 and M0205350 did notshow sterility across all populations. Nearly all lines with a CĆAA orTTAA haplotype had at least 10% of plants that showed sterility. It isnot unexpected that some plants in these lines did no show sterility assome variation in the spray application or other environmentalvariations can influence the expression of sterility. Lines genotyped asCTAT or TTAT were segregating at the dicamba tolerance locus and progenyfrom these lines showed a range of response for sterility.

These results support the observations that certain haplotypes at thedicamba tolerance locus in lines containing the RR2Y CP4 and DMOtransgenes causes sterility from glyphosate applications made at the V6plant stage.

Example 4 Exemplary Marker Assays for Detecting Polymorphisms

In one embodiment, the detection of polymorphic sites in a sample ofDNA, RNA, or cDNA may be facilitated through the use of nucleic acidamplification methods. Such methods specifically increase theconcentration of polynucleotides that span the polymorphic site, orinclude that site and sequences located either distal or proximal to it.Such amplified molecules can be readily detected by gel electrophoresis,fluorescence detection methods, or other means. Exemplary primers andprobes for amplifying and detecting genomic regions associated with adicamba tolerance phenotype are given in Table 11.

TABLE 11 Exemplary Assays for Detecting Polymorphisms SEQ ID SEQ IDMarker NO NO SEQ ID Marker or SEQ NO SNP Forward Reverse NO SEQ ID NOLocus Name ID: Position Primer Primer Probe 1 Probe 2 asmbl_11856 1TC122822 2 BI967232 3 M0205928 4 M0101742³ 5 1206 24 25 26 27 M0129138 6218 28 29 30 31 BU551345 7 M0114388 8 502 32 33 34 35 BU551363 9M0205350⁴ 10 148 36 37 38 39 M0102027⁵ 11 349 40 41 42 43 BU765955 12M0093116 13 183 44 45 46 47 M0129925 14 328 48 49 50 51 M0205537 15M0202715 16 M0206286 17 M0206054 18 M0205375 19 NGMAX008197032 52 201 5354 55 56

Example 5 Oligonucleotide Probes Useful for Detecting Polymorphisms bySingle Base Extension Methods

Oligonucleotides can also be used to detect or type the polymorphismsdisclosed herein by single base extension (SBE)-based SNP detectionmethods. Exemplary oligonucleotides for use in SBE-based SNP detectionare provided in Table 12. SBE methods are based on extension of anucleotide primer that is hybridized to sequences adjacent to apolymorphism to incorporate a detectable nucleotide residue uponextension of the primer. It is also anticipated that the SBE method canuse three synthetic oligonucleotides. Two of the oligonucleotides serveas PCR primers and are complementary to the sequence of the locus whichflanks a region containing the polymorphism to be assayed. Exemplaryextension primers that can be used to type polymorphisms disclosed inthis invention are provided in Table 12 in the column labeled “Probe(SBE)”. Following amplification of the region containing thepolymorphism, the PCR product is hybridized with an extension primerwhich anneals to the amplified DNA adjacent to the polymorphism. DNApolymerase and two differentially labeled dideoxynucleosidetriphosphates are then provided. If the polymorphism is present on thetemplate, one of the labeled dideoxynucleoside triphosphates can beadded to the primer in a single base chain extension. The allele presentis then inferred by determining which of the two differential labels wasadded to the extension primer. Homozygous samples will result in onlyone of the two labeled bases being incorporated and thus only one of thetwo labels will be detected. Heterozygous samples have both allelespresent, and will thus direct incorporation of both labels (intodifferent molecules of the extension primer) and thus both labels willbe detected. Exemplary forward and reverse SBE probes are provided inTable 12.

TABLE 12 Exemplary SBE Probes for Detecting PolymorphismsMarker or Locus Marker SNP Probe Name (SEQ ID NO) Position Probe (SBE)(SEQ ID NO) M0101742  5 1206 TGACTAGCATGTATCTAT 26 ATGACTAACATGTATCTAT27 M0129138  6 218 TGTGTCCTATATGATCTT 30 TGTCCTGTATGATCTTA 31 M0114388 8 502 AGTTGGGCTATGCAA 34 TGGGCTGTGCAAGTA 35 M0205350 10 148AGTTTACACTTACAAATATT 38 AGAGTTTACACTTACATATATT 39 M0102027 11 349ACCCCCCTTTTTT 42 ATTTTAACCCCCTTTTT 43 M0093116 13 183 CCAACACCAAACTA 46CAACACCAAACAAA 47 M0129925 14 328 AGTAGTAGCTAGTGAAATA 50AGCTAGTCAAATATTT 51 NGMAX008197032 52 201 TTGACAGCCTCTGGATAT 55ACAGCCTCCGGATAT 56

Example 6 Haplotypes Associated with a Malformation and SterilityPhenotypes in MG 4 Populations Upon Herbicide Application

The effect of different haplotypes on response to dicamba and glyphosatewere evaluated by comparing genetically similar lines that contained aCP4 transgene that confers tolerance to glyphosate and a DMO transgenethat confers tolerance to dicamba. In 2010, two plants from each offourteen BC1F2:4 lines, or families, across five backcross populationswere harvested individually to develop pairs of BC1F4:6 lines from eachfamily. The haplotype of each recurrent parent for each backcrosspopulation is shown in Table 13.

TABLE 13 Haplotypes Associated With Listed Recurrent Parent. BackcrossRecurrent parent haplotype population Recurrent parent M0101742 M0205350M0102027 1 CBL3606Q0R CC AA TT 2 AG4005 CC AA TT 3 CP4408A3-C0RN CC AATT 4 AG4907 CC AA TT 5 AG4630 TT AA TT

The donor parent for each population was A3244-RR2Y/A3525-DT that had aTTTTCC haplotype for markers M0101742, M0205350, and M0102027 markers,respectively. During the breeding process, the haplotype for each lineat the dicamba tolerance locus was not known. Markers were used toselect for the absence of the RR1 CP4 gene, and for the presence of theRR2Y CP4 gene and the Dicamba DMO gene. The BC1F4:5 rows were sprayedwith glyphosate at the V6 plant growth stage in Quillota Chile where apair of lines per family were rated for sterility to glyphosate. Table14 describes the breeding history for this plant material.

TABLE 14 Breeding History for Plant Material in Example 6. Gen. SeasonYear Location Breeding Activity Cross Winter 2007 Isabella, Puerto RicoCross F1 Summer 2008 Isabella, Puerto Rico Backcross BC1F1 Winter 2008Isabella, Puerto Rico Bulk BC1F2 Summer 2009 Evansville, IN, Singleplant selection Stonington, IL, or Galena, MD BC1F2: Summer 2010Fontezuela, Argentina Progeny row 3 BC1F2: Summer 2010 Evansville, IN,Single plant selection 4 Stonington, IL, or Galena, MD BC1F4: Summer2011 Quillota, Chile Progeny row 5 BC1F4: Summer 2011 Evansville, IN,Spray trials 6 Stonington, IL, Galena, MD, and Stuttgart, AR

DNA was extracted from each line to generate haplotypes across threemarkers at the dicamba tolerance locus. The lines were evaluated acrossfour locations in the United States (Stuttgart, Ark.; Stonington Ill.;Evansville, Ind.; and Galena, Md.) in 2011. At each location the lineswere grown in four to five foot single-row plots replicated two timesand one of seven different herbicide treatments were applied atdifferent plant growth stages (V3 or V6) as described in Table 15.

TABLE 15 Herbicide Treatments (Glyphosate and Dicamba) andConcentrations Applied at Plant Growth Stages (V3 or V6). HerbicideTreatment Glyphosate Dicamba Glyphosate Dicamba Number V3 V3 V6 V6 1none none none none 2 0.75 lb none none none a.e./acre 3 0.75 lb none1.5 lb none a.e./acre a.e./acre 4 none 1.0 lb none none a.e./acre 5 none1.0 lb none 1.0 lb a.e./acre a.e./acre 6 0.75 lb 1.0 lb none nonea.e./acre a.e./acre 7 0.75 lb 1.0 lb 1.5 lb 1.0 lb a.e./acre a.e./acrea.e./acre a.e./acre

Rating Scale:

Malformation to dicamba was rated by the percentage of plants showingmalformation Sterility to glyphosate was rated as:A rating scale of 1: Less than 10% of plants show sterilityA rating scale of 2: Less than 10-50% of plants show sterilityA rating scale 3: Greater than 50% of plants show sterility

Data were averaged across replications and locations to place intofollowing classes as described in Table 16.

TABLE 16Haplotypes Associated with a Malformation and Sterility Phenotypes in SoybeanSister Line Pedigrees in Response to Herbicide Treatment Protocols.Reaction to Glyphosate in Treatment No. Back-cross Quillota,Marker haplotype 1 2 3 4 5 6 7 Population Family Chile M0101742 M0205350M0102027 Response 1 1.1 N TT TT CC N N N N N N N S CC AA TT N N S N M NM/S 2 2.1 S CC AA TT N N S N M S M/S S CC AA TT N N S N M N M/S 3 3.1 NTT TT CC N N N N N N N S CC AA TT N N S N M N M/S 4 4.1 S CC AA TT N N SN M N M/S N TT TT CC N N N N N N N 4.2 S CC AA TT N N S N M N M/S S CCAA TT N N S N M N M/S 4.3 S CC AA TT N N S N M N M/S S CC AA TT N N S NM N M/S 4.4 S CC AA TT N N S N M N M/S S CC AA TT N N S N M N M/S 4.5 SCC AA TT N N S N M N M/S S CC AA TT N N S N M N M/S 4.6 N TT TT CC N N NN N N N N TT TT CC N N N N N N N 4.7 N TT TT CC N N N N N N N S CC AA TTN N S N M N M/S 4.8 S CC AA TT N N S N M N M/S S CC AA TT N N S N M NM/S 4.9 S CC AA TT N N S N M N M/S S CC AA TT N N S N M N M/S 4.10  S CCAA TT N N S N M N M/S S CC AA TT N N S N M N M/S 5 5.1 S TT AA TT N N SN M N M/S N TT TT CC N N N N N N N N = normal response to treatment:Average <1/= 1.25 sterility and/or </= 30% malformation S = sterility toa glyphosate treatment: Average >1.25 M = malformation to a dicambatreatment >30% malformation M/S = malformation dicamba and sterility toglyphosate in a combination treatment

Example 7 Selection for Absence of Sterility to Glyphosate Applicationand Recovery of the Favorable Haplotype

As described in Example 3, marker haplotypes corresponded to reaction toglyphosate application. There were several populations grown inFontezuela, Argentina where plants sprayed with glyphosate were selectedfor reproductive tolerance to glyphosate in the absence of haplotypeinformation on each line. Table 17 describes four populations thatsegregated for the haplotype based on parental haplotypes. Table 18describes the number of lines grown and the number of lines selected.

TABLE 17Four soybean populations that segregated for the preferred haplotypebased on parental haplotypes. Parent 1 Parent 2 NGMAX- M- NGMAX- M-008197032 0205350 008197032 0205350 Population Origin (SEQ ID NO: 52)(SEQ ID NO: 10) (SEQ ID NO: 52) (SEQ ID NO: 10) 1 AG4031/AG38 GG AA AATT 03-T0BAH 2 AG4130/AG49 AA TT GG AA 07-T0BAH 3 BL3510A9- AA TT GG AAD0AAC/AG49 07-T0BAH 4 EI4409C3- GG AA AA TT D0YN/GL4807 A2-D0RN- T0BAH

TABLE 18 Number of soybean lines grown and the number of soybean linesselected. Population No. Lines Grown No. Lines Selected 1 165 2 2 92 9 3200 10 4 260 25 Total 717 46

The 46 selected lines were subsequently genotyped and found to possessthe favorable AATT haplotype. In addition, the lines were grown atStonington, Ill. in 2012 and evaluated for herbicide response. The lineswere sprayed with 1.0 lb a.e/acre dicamba and 1.5 lb a.e/acre glyphosateat the V6 plant stage and did not show malformation to dicamba orsterility to glyphosate. These results further support the ability touse glyphosate selection as a means to recover the favorable haplotypeand tolerance to both glyphosate and dicamba.

Example 8 Comparison of Dicamba Tolerance in Different HaplotypesContaining a Dicamba Resistance Conferring Transgene

The effect of different haplotypes on response to dicamba was evaluatedby comparing F2 families that contained the DMO transgene for dicambaresistance, but that lacked the CP4 transgene for glyphosate resistance.F2 plants across six different populations that were growing in Kunia,Hi. in 2012 were tissue sampled and genotyped for the CP4 and DMOtransgenes and for markers NGMAX008197032 and M0205350. F2 plants thatwere fixed homozygous for the presence of DMO and absence of CP4 andthat were fixed homozygous for a haplotype class were selected andharvested individually to create families. Table 19 shows the number ofF2 families per haplotype class. The F2 families were evaluated fortolerance to dicamba in a greenhouse environment.

TABLE 19Six soybean populations that segregated for the preferred haplotypebased on parental haplotypes. Haplotype Class AATT¹ GGAA² POP ORIGINNumber of F2 plants 5 A3525-A3244-BAH/A3431 8 10  6DKB31-51/A3525-A3244-BAH 3 3 8 AG4903/A3525-A3244-BAH 0 3 9AG4907/A3525-A3244-BAH 2 2 12  AG4903/(AG4903*2/A3525-A3244-BAH) 0 5 13 AG4907/GL4911A9-B0BAH 0 5 ¹An “AA” allele for NGMAX-008197032 (SEQ IDNO: 52) and a “TT” allele for M020535(SEQ ID NO: 10) (i.e. “favorable”haplotype for dicamba tolerance). ²A “GG” allele for NGMAX-008197032(SEQ ID NO: 52) and an “AA” allele for M020535(SEQ ID NO: 10) (i.e.“unfavorable” haplotype for dicamba tolerance).

A comparison of dicamba tolerance in the plants from segregatingpopulations of Table 19 having various “favorable” or “unfavorable”haplotypes of the indicated parental germplasm is provided in FIG. 1.Plants having the favorable haplotypes (i.e. an “AA” allele forNGMAX-008197032 (SEQ ID NO:52) and a “TT” allele for M020535 (SEQ ID NO:10) showed consistently low dicamba injury (FIG. 1).

Example 9 Selection of Favorable Dicamba Tolerance Haplotypes with Oneor Two Spray Treatments

A comparison of selections of favorable and unfavorable dicambatolerance haplotypes based on either one or two spray treatments wasmade. Transgenic soybean plants containing a dicamba resistanceconferring transgene and various favorable or unfavorable haplotypeswere treated with dicamba at a rate of 1 pound/acre at either: (a) theV3 and V6 stages; or (b) the V6 stage only. The results of thiscomparison are shown in FIG. 2. Selection of favorable haplotypes byusing a single spray at V6 (dicamba 1 lb/a) was found to be as effectiveas selections with the combination of aV3 and a V6 spray treatment.

Having illustrated and described the principles of the presentinvention, it should be apparent to persons skilled in the art that theinvention can be modified in arrangement and detail without departingfrom such principles.

Although the materials and methods of this invention have been describedin terms of various embodiments and illustrative examples, it will beapparent to those of skill in the art that variations can be applied tothe materials and methods described herein without departing from theconcept, spirit and scope of the invention. All such similar substitutesand modifications apparent to those skilled in the art are deemed to bewithin the spirit, scope and concept of the invention as defined by theappended claims.

TABLE 2 of the Specification Locus/Display Start End ADDITIONAL LOCUSName (1) Source (2) Base (3) Base (4) INFORMATION (5) asmbl_11856Vigna_(—) 16426 16586 SEQ ID NO: 1 unguiculata TA2790_3886 Phaseolus_(—)16423 17393 ADP-ribosylation factor coccineus_(—) [Vigna unguiculatarelease_2 (Cowpea)] TA43459_3847 Glycine_(—) 16434 18055ADP-ribosylation factor 1 max_release_(—) [Oryza sativa (Rice)] 2TC276541 GMGI.071508 16434 18076 UniRef100_P36397 Cluster:ADP-ribosylation factor 1; n = 1; Arabidopsis thaliana|Rep: ADP-ribosylation factor 1 - Arabidopsis thaliana (Mouse-ear cress) = partial(38%) CD392203 Glycine_(—) 16216 18687 ADP-ribosylation factormax_release_(—) [Glycine max (Soybean)] 2 BQ610865 Glycine_(—) 1632718667 ADP-ribosylation factor 1 max_release_(—) [Oryza sativa (Rice)] 2EH046324 Arachis_(—) 16405 18745 Cluster: ADP-ribosylationstenosperma_(—) factor 1, n = 1, Arabidopsis release_5 thaliana|Rep:ADP- ribosylation factor 1 - Arabidopsis thaliana (Mouse-ear cress)AW202311 Glycine_(—) 16378 19070 ADP-ribosylation factor max_release_(—)[Glycine max (Soybean)] 2 TC242702 GMGI.071508 16234 20195UniRef100_Q38JU3 Cluster: ADP ribosylation factor 002; n = 2; coreeudicotyledons|Rep: ADP ribosylation factor 002 - Daucus carota (Carrot)= complete BI321678 Glycine_(—) 17384 19066 ADP-ribosylation factormax_release_(—) [Zea mays (Maize)] 2 AW348317 Glycine_(—) 16355 20097ADP-ribosylation factor max_release_(—) [Glycine max (Soybean)] 2EH042959 Arachis_(—) 16401 20182 Cluster: ADP-ribosylationstenosperma_(—) factor 1, n = 2, release_5 Medicago|Rep: ADP-ribosylation factor 1 - Medicago truncatula (Barrel medic) TC20337LJGI.070108 16420 20191 UniRef100_Q5QQ33 Cluster: ADP-ribosylationfactor 1, n = 2, Medicago|Rep: ADP- ribosylation factor 1 - Medicagotruncatula (Barrel medic), complete EH047563 Arachis_(—) 16430 20182Cluster: ADP-ribosylation stenosperma_(—) factor 1, n = 2, release_5Medicago|Rep: ADP- ribosylation factor 1 - Medicago truncatula (Barrelmedic) TA2789_3886 Phaseolus_(—) 16436 20196 ADP-ribosylation factor 1-coccineus_(—) like protein [Solanum release_2 tuberosum (Potato)]TA43462_3847 Glycine_(—) 16229 20438 ADP-ribosylation factormax_release_(—) [Medicago sativa (Alfalfa)] 2 TA1120_34305 Lotus_(—)16522 20191 ADP-ribosylation factor japonicus_(—) [Medicago sativa(Alfalfa)] release_1 TA2306_3848 Glycine_(—) 16442 20440ADP-ribosylation factor soja_release_(—) [Medicago sativa (Alfalfa)] 2TC273941 GMGI.071508 16426 20464 homologue to UniRef100_Q38JU3 Cluster:ADP ribosylation factor 002; n = 2; core eudicotyledons|Rep: ADPribosylation factor 002 - Daucus carota (Carrot) = complete TC238119GMGI.071508 16455 20449 UniRef100_Q38JU3 Cluster: ADP ribosylationfactor 002; n = 2; core eudicotyledons|Rep: ADP ribosylation factor002 - Daucus carota (Carrot) = complete EG373880 Arachis_(—) 17101 20182Cluster: ADP-ribosylation hypogaea_(—) factor 1, n = 2, release_5Medicago|Rep: ADP- ribosylation factor 1 - Medicago truncatula (Barrelmedic) BF066818 Glycine_(—) 17081 20378 ADP-ribosylation factor 1max_release_(—) [Populus tomentosa] 2 BF596154 Glycine_(—) 17083 20397ADP-ribosylation factor max_release_(—) [Hyacinthus orientalis 2 (Commonhyacinth)] AW760997 Glycine_(—) 17116 20397 ADP-ribosylation factormax_release_(—) [Hyacinthus orientalis 2 (Common hyacinth)] BF424079Glycine_(—) 17112 20417 ADP-ribosylation factor max_release_(—)[Hyacinthus orientalis 2 (Common hyacinth)] AW596022 Glycine_(—) 1712120415 ADP-ribosylation factor 1 max_release_(—) [Populus tomentosa] 2TA43446_3847 Glycine_(—) 17106 20436 ADP-ribosylation factormax_release_(—) [Hyacinthus orientalis 2 (Common hyacinth)] TA43455_3847Glycine_(—) 17125 20452 ADP-ribosylation factor max_release_(—)[Hyacinthus orientalis 2 (Common hyacinth)] BW595867 Lotus_(—) 1741820191 ADP-ribosylation factor japonicus_(—) [Hyacinthus orientalisrelease_1 (Common hyacinth)] AW507598 Glycine_(—) 17343 20437ADP-ribosylation factor max_release_(—) [Hyacinthus orientalis 2 (Commonhyacinth)] TA43447_3847 Glycine_(—) 17343 20445 ADP-ribosylation factormax_release_(—) [Hyacinthus orientalis 2 (Common hyacinth)] TA43448_3847Glycine_(—) 17355 20438 ADP-ribosylation factor 1 max_release_(—)[Populus tomentosa] 2 AW596189 Glycine_(—) 17358 20442 ADP-ribosylationfactor 1 max_release_(—) [Populus tomentosa] 2 BI469983 Glycine_(—)17410 20438 ADP-ribosylation factor 1 max_release_(—) [Populustomentosa] 2 AW472058 Glycine_(—) 18655 20160 ADP-ribosylation factor 1max_release_(—) [Daucus carota (Carrot)] 2 CB063805 Glycine_(—) 1862320432 ADP-ribosylation factor 1 max_release_(—) [Populus tomentosa] 2BM891090 GMGI.071508 18995 20429 homologue to UniRef100_A7PRL9 Cluster:Chromosome chr14 scaffold_27 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr14 scaffold_27 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (42%) BM731935 Glycine_(—)19949 20444 ADP-ribosylation factor 1 max_release_(—) [Populustomentosa] 2 AW695591 MTGI.071708 30054 31388 similar toUniRef100_Q40542 Cluster: NPK2, n = 1, Nicotiana tabacum|Rep: NPK2 -Nicotiana tabacum (Common tobacco), partial (35%) TC130040 MTGI.07170830054 31482 similar to UniRef100_A7PM42 Cluster: Chromosome chr14scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep:Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitisvinifera (Grape), partial (30%) TC122822 MTGI.071708 30054 34162 Proteinkinase, Nuclear transport factor 2. SEQ ID NO: 2 Pvcon9203 Phaseolus_(—)31194 34247 UniRef100_A7PM42 vulgaris Chromosome chr14 scaffold_21,whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID =A7PM42_VITVI E-0 TA66103_3847 Glycine_(—) 31879 34559 Protein kinase;Nuclear max_release_(—) transport factor 2 2 [Medicago truncatula(Barrel medic)] CA801261 GMGI.071508 33896 34304 similar toUniRef100_Q40542 Cluster: NPK2; n = 1; Nicotiana tabacum|Rep: NPK2 -Nicotiana tabacum (Common tobacco) = partial (16%) TC120073 MTGI.07170835367 38178 Glycoside hydrolase, family 28 NP004759 GMGI.071508 3497639622 GB|AF128266.1|AAD4648 3.1 polygalacturonase PG1 AF128266Glycine_(—) 34980 39622 Polygalacturonase PG1 max_release_(—) [Glycinemax (Soybean)] 2 TA69799_3847 Glycine_(—) 58988 65870Ubiquitin-associated max_release_(—) [Medicago truncatula 2 (Barrelmedic)] TA7619_47247 Lotus_(—) 63855 65940 Putative DNA cytosinecorniculatus_(—) methyltransferase Zmet3 release_1 related clusterTA8711_34305 Lotus_(—) 63855 65940 UBA-like [Medicago japonicus_(—)truncatula (Barrel medic)] release_1 TC34762 LJGI.070108 65619 65940 NAPvcon5587 Phaseolus_(—) 65216 67090 UniRef100_A7PM76 vulgaris Chromosomechr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitisvinifera RepID = A7PM76_VITVI E-0 TA5046_3885 Phaseolus_(—) 65808 67002UBA-like [Medicago vulgaris_(—) truncatula (Barrel medic)] release_2asmbl_11857 Vigna_(—) 65951 67042 NA unguiculata TA58707_3847Glycine_(—) 66006 67253 UBA-like [Medicago max_release_(—) truncatula(Barrel medic)] 2 TC241193 GMGI.071508 66006 67253 similar toUniRef100_A7PM76 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (38%) BI967232 Glycine_(—) 66170 67203 UBA-like [Medicagomax_release_(—) truncatula (Barrel 2 medic)]. SEQ ID NO: 3 AV417590LJGI.070108 66745 67090 similar to UniRef100_A7PM76 Cluster: Chromosomechr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitisvinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgunsequence - Vitis vinifera (Grape), partial (19%) AV768315 Lotus_(—)66699 67155 UBA-like [Medicago japonicus_(—) truncatula (Barrel medic)]release_1 TC32114 LJGI.070108 66699 67275 similar to UniRef100_Q76KU6Cluster: DNA methyltransferase, n = 1, Nicotiana tabacum|Rep: DNAmethyltransferase - Nicotiana tabacum (Common tobacco), partial (20%)TA1535_34305 Lotus_(—) 66745 67277 UBA-like [Medicago japonicus_(—)truncatula (Barrel medic)] release_1 TA2793_47247 Lotus_(—) 66745 67277DNA methyltransferase corniculatus_(—) related cluster release_1AV768911 Lotus_(—) 66943 67155 Ubiquitin-associated japonicus_(—)[Medicago truncatula release_1 (Barrel medic)] CB540531 Phaseolus_(—)73267 73561 UniRef100_A7PM74 vulgaris Chromosome chr14 scaffold_21,whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID =A7PM74_VITVI 5.00E−27 BE347690 GMGI.071508 73509 73770 similar toUniRef100_Q5VQL1-2 Cluster: Isoform 2 of Q5VQL1; n = 1; Oryza sativaJaponica Group|Rep: Isoform 2 of Q5VQL1 - Oryza sativa subsp. japonica(Rice) = partial (5%) BE347690 Glycine_(—) 73509 73822 WW/Rsp5/WWP;max_release_(—) Helicase = C-terminal 2 [Medicago truncatula (Barrelmedic)] BE608496 GMGI.071508 73444 73947 similar to UniRef100_A7PM74Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n= 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence - Vitis vinifera (Grape) = partial (16%) AI416763GMGI.071508 74073 74520 similar to UniRef100_Q9SP26 Cluster: P72 DEADbox protein; n = 1; Pisum sativum|Rep: P72 DEAD box protein - Pisumsativum (Garden pea) = partial (16%) AI416763 Glycine_(—) 74073 74743ATP-dependent RNA max_release_(—) helicase-like protein DB10 2[Nicotiana sylvestris (Wood tobacco)] BW615083 LJGI.070108 74256 74855similar to UniRef100_A7PM74 Cluster: Chromosome chr14 scaffold_21, wholegenome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape),partial (24%) TA8332_34305 Lotus_(—) 74256 75446 WW/Rsp5/WWP, Helicase,japonicus_(—) C-terminal [Medicago release_1 truncatula (Barrel medic)]TC27807 LJGI.070108 74343 75446 similar to UniRef100_Q9SP26 Cluster: P72DEAD box protein, n = 1, Pisum sativum|Rep: P72 DEAD box protein - Pisumsativum (Garden pea), partial (34%) asmbl_11858 Vigna_(—) 75228 75500 NAunguiculata TA60825_3847 Glycine_(—) 74963 75981 P72 DEAD box proteinmax_release_(—) [Pisum sativum (Garden 2 pea)] TC249436 GMGI.07150874985 75966 similar to UniRef100_Q9SP26 Cluster: P72 DEAD box protein; n= 1; Pisum sativum|Rep: P72 DEAD box protein - Pisum sativum (Gardenpea) = partial (12%) TC269249 GMGI.071508 86882 87576 similar toUniRef100_A7PM72 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (42%) TA64136_3847 Glycine_(—) 86882 89066 Putativemax_release_(—) phosphate/phosphoenol- 2 pyruvate translocator[Arabidopsis thaliana (Mouse-ear cress)] CO982132 Glycine_(—) 8722591497 Phosphate/phosphoenol- max_release_(—) pyruvate translocator 2[Nicotiana tabacum (Common tobacco)] TC274531 GMGI.071508 87225 91497similar to UniRef100_A4UTS3 Cluster: Chloroplast phosphoenolpyruvate/phosphate translocator; n = 1; Pisum sativum|Rep: Chloroplastphosphoenol- pyruvate/phosphate translocator - Pisum sativum (Gardenpea) = partial (53%) Pvcon2802 Phaseolus_(—) 87119 92616UniRef100_A9PD12 vulgaris Putative uncharacterized protein n = 1 Tax =Populus trichocarpa RepID = A9PD12_POPTR 1.00E−121 TA4406_3885Phaseolus_(—) 89055 92616 Phosphate/phosphoenol- vulgaris_(—) pyruvatetranslocator release_2 [Nicotiana tabacum (Common tobacco)] TA74766_3847Glycine_(—) 91397 92725 Phosphoenolpyruvate/ max_release_(—) phosphatetranslocator 2 [Mesembryanthemum crystallinum (Common ice plant)]TC265023 GMGI.071508 91686 92725 similar to UniRef100_A7PM71 Cluster:Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (15%) M0205928 SEQ. 9271892334 SEQ ID NO: 4 LISTING BG406195 GMGI.071508 107039 107366 BG406195Glycine_(—) 107039 107375 NA max_release_(—) 2 M0101742 SEQ. 112189113483 SEQ ID NO: 5 LISTING BG550728 GMGI.071508 112663 113757 weaklysimilar to UniRef100_A7PM60 Cluster: Chromosome chr14 scaffold_21 =whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomechr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (13%) BG550728 Glycine_(—) 112663 113867 Receptor-likemax_release_(—) serine/threonine kinase 2 [Arabidopsis thaliana(Mouse-ear cress)] CV535605 Phaseolus_(—) 112548 113982 UniRef100_A7PM60vulgaris Chromosome chr14 scaffold_21, whole genome shotgun sequence n =1 Tax = Vitis vinifera RepID = A7PM60_VITVI 9.00E−79 M0129138 SEQ.114532 113494 SEQ ID NO: 6 LISTING BU551345 Glycine_(—) 115956 116339SEQ ID NO: 7 max_release_(—) 2 TA58315_3847 Glycine_(—) 118318 120087 NAmax_release_(—) 2 TC236438 GMGI.071508 118318 120087 NA BE611751Glycine_(—) 119165 119645 NA max_release_(—) 2 BE611751 GMGI.071508119229 119645 NA TA70371_3847 Glycine_(—) 137417 137864 Hypotheticalprotein max_release_(—) [Medicago truncatula 2 (Barrel medic)] TC267549GMGI.071508 137417 137864 similar to UniRef100_Q9FI64 Cluster: GenomicDNA = chromosome 5 = TAC clone: K21I16; n = 1; Arabidopsis thaliana|Rep:Genomic DNA = chromosome 5 = TAC clone: K21I16 - Arabidopsis thaliana(Mouse-ear cress) = partial (43%) BG156330 GMGI.071508 155872 156903similar to UniRef100_A7PM41 Cluster: Chromosome chr14 scaffold_21 =whole genome shotgun sequence; n = 2; Vitis vinifera|Rep: Chromosomechr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (23%) BG156330 Glycine_(—) 155872 157058 WD40-like[Medicago max_release_(—) truncatula (Barrel medic)] 2 Pvcon10326Phaseolus_(—) 155691 157835 UniRef100_A7PM41 vulgaris Chromosome chr14scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis viniferaRepID = A7PM41_VITVI 3.00E−93 CD397113 Glycine_(—) 157474 157813 NAmax_release_(—) 2 TA12653_34305 Lotus_(—) 159489 161341 NADP-specificisocitrate japonicus_(—) dehydrogenase [Lupinus release_1 albus (Whitelupin)] TC27381 LJGI.070108 159489 161341 similar to UniRef100_Q7Y0W7Cluster: NADP-specific isocitrate dehydrogenase, n = 1, Lupinusalbus|Rep: NADP-specific isocitrate dehydrogenase - Lupinus albus (Whitelupin), partial (25%) DT084057 Glycine_(—) 161638 162192 NADP-specificisocitrate soja_release_(—) dehydrogenase [Lupinus 2 albus (Whitelupin)] BE661051 Glycine_(—) 170271 172034 Cyclin-like F-boxmax_release_(—) [Medicago truncatula 2 (Barrel medic)] TA11305_34305Lotus_(—) 170700 172307 Cyclin-like F-box japonicus_(—) [Medicagotruncatula release_1 (Barrel medic)] TC34049 LJGI.070108 170700 172307similar to UniRef100_A7PF14 Cluster: Chromosome chr11 scaffold_13, wholegenome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr11scaffold_13, whole genome shotgun sequence - Vitis vinifera (Grape),partial (32%) NP7256876 MTGI.071708 171929 173188 GB|AC157983.16|ABE86510.1 Cyclin-like F-box TA68495_3847 Glycine_(—) 194920 195696 Oleosin[Sesamum indicum max_release_(—) (Oriental sesame) 2 (Gingelly)]TC265354 GMGI.071508 194920 195696 weakly similar to UniRef100_P29530Cluster: P24 oleosin isoform A; n = 1; Glycine max|Rep: P24 oleosinisoform A - Glycine max (Soybean) = partial (40%) BE658264 Glycine_(—)195176 195925 Oleosin [Sesamum indicum max_release_(—) (Oriental sesame)2 (Gingelly)] CV539661 Phaseolus_(—) 217885 218101 No significant hit(e-20) vulgaris CA912681 Phaseolus_(—) 220374 220748 Arabidopsisthaliana coccineus_(—) genomic DNA, release_2 chromosome 3, P1 clone:MGF10 [Arabidopsis thaliana (Mouse-ear cress)] CA785107 Glycine_(—)221393 221885 NA soja_release_(—) 2 TC276537 GMGI.071508 221407 222104weakly similar to UniRef100_Q4RYK7 Cluster: Chromosome 3 SCAF14975 =whole genome shotgun sequence; n = 1; Tetraodon nigroviridis|Rep:Chromosome 3 SCAF14975 = whole genome shotgun sequence - Tetraodonnigroviridis (Green puffer) = partial (21%) TA71044_3847 Glycine_(—)221407 222133 NA max_release_(—) 2 CD406643 Glycine_(—) 222113 222297 NAmax_release_(—) 2 AV416316 LJGI.070108 223773 223869 similar toUniRef100_A7PM35 Cluster: Chromosome chr14 scaffold_21, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape),partial (9%) EC911350 Phaseolus_(—) 224587 225958 UniRef100_A5C233vulgaris Putative uncharacterized protein n = 1 Tax = Vitis viniferaRepID = A5C233_VITVI 3.00E−77 BU760697 GMGI.071508 224857 225965 similarto UniRef100_A7PM35 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (22%) BU760697 Glycine_(—) 224857 226145 Protein At5g19130max_release_(—) [Arabidopsis thaliana 2 (Mouse-ear cress)] TC119982MTGI.071708 224248 226812 Gaa1-like, GPI transamidase component CV541515Phaseolus_(—) 225934 226374 UniRef100_A7PM35 vulgaris Chromosome chr14scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis viniferaRepID = A7PM35_VITVI 2.00E−34 TA76349_3847 Glycine_(—) 226118 226768Protein At5g19130 max_release_(—) [Arabidopsis thaliana 2 (Mouse-earcress)] TA12045_47247 Lotus_(—) 226354 226789 GPAA1-like protein relatedcorniculatus_(—) cluster release_1 TA13675_34305 Lotus_(—) 226354 226789Protein At5g19130 japonicus_(—) [Arabidopsis thaliana release_1(Mouse-ear cress)] TC29330 LJGI.070108 226354 226789 similar toUniRef100_A7PM35 Cluster: Chromosome chr14 scaffold_21, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape),partial (13%) NP7254537 MTGI.071708 233411 237212GB|AC152349.11|ABP03404.1 Protein of unknown function DUF266, plantEH256962 GMGI.071508 235306 237649 similar to UniRef100_A7PM54 Cluster:Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (33%) CX708677 Glycine_(—)247269 248145 NA max_release_(—) 2 BW599077 LJGI.070108 255475 261945similar to UniRef100_A7QD90 Cluster: Peptidyl-prolyl cis- transisomerase, n = 1, Vitis vinifera|Rep: Peptidyl- prolyl cis-transisomerase - Vitis vinifera (Grape), partial (18%) BW625918 LJGI.070108257810 262980 similar to UniRef100_Q93YQ8 Cluster: Peptidyl-prolyl cis-trans isomerase, n = 1, Arabidopsis thaliana|Rep: Peptidyl-prolylcis-trans isomerase - Arabidopsis thaliana (Mouse-ear cress), partial(32%) DT083826 Glycine_(—) 260886 261121 NA soja_release_(—) 2 CB063628GMGI.071508 271592 271900 similar to UniRef100_A7PM52 Cluster:Chromosome chr14 scaffold_21 whole genome shotgun sequence; n = 1; Vitisvinifera|Rep: = partial (2%) CB063628 Glycine_(—) 271592 271928 NAmax_release_(—) 2 TA5835_34305 Lotus_(—) 273868 275906 Vegetative cellwall protein japonicus_(—) gp1-like [Oryza sativa release_1 (japonicacultivar-group) TC32024 LJGI.070108 275152 275906 similar toUniRef100_A7PM52 Cluster: Chromosome chr14 scaffold_21, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape),partial (9%) TC252667 GMGI.071508 275739 276506 similar toUniRef100_A7PM52 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (12%) AW311416 Glycine_(—) 276269 276455 NA max_release_(—) 2WmFPC_(—) 99810 475910 NA Contig850 CV534998 Phaseolus_(—) 288050 288585UniRef100_A7PM50 vulgaris Chromosome chr14 scaffold_21, whole genomeshotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM50_VITVI6.00E−39 TA75806_3847 Glycine_(—) 288290 290376 Arabidopsis thalianamax_release_(—) genomic DNA = 2 chromosome 3 = P1 clone: MGF10[Arabidopsis thaliana (Mouse-ear cress)] TC276120 GMGI.071508 288290290376 similar to UniRef100_A7PM50 Cluster: Chromosome chr14 scaffold_21= whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomechr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (62%) BI786388 GMGI.071508 291666 292088 similar toUniRef100_A7PM49 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (7%) BI786388 Glycine_(—) 291666 292099 NA max_release_(—) 2TA63308_3847 Glycine_(—) 291633 294397 NA max_release_(—) 2 TC243765GMGI.071508 293681 294426 weakly similar to UniRef100_Q0JDM0 Cluster:Os04g0394300 protein; n = 1; Oryza sativa Japonica Group|Rep:Os04g0394300 protein - Oryza sativa subsp. japonica (Rice) = partial(3%) TA6412_34305 Lotus_(—) 293803 294412 NA japonicus_(—) release_1TC24112 LJGI.070108 293803 294412 NA CA899930 Phaseolus_(—) 294054294263 NA coccineus_(—) release_2 TA3887_3886 Phaseolus_(—) 302301303033 Hypothetical protein coccineus_(—) MJH23.3 [Arabidopsis release_2thaliana (Mouse-ear cress)] AW705271 Glycine_(—) 302299 303855Hypothetical protein max_release_(—) MJH23.3 [Arabidopsis 2 thaliana(Mouse-ear cress)] TC237313 GMGI.071508 303227 306007 similar toUniRef100_A7PM30 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (54%) TA61594_3847 Glycine_(—) 303227 306056 Similarity to RNAbinding max_release_(—) protein [Arabidopsis 2 thaliana (Mouse-earcress)] asmbl_11859 Vigna_(—) 303952 305921 NA unguiculata toGm05DAGchainer 30059 580791 Ks0.2335 BU544029 Glycine_(—) 305220 305762 NAmax_release_(—) 2 TC23280 LJGI.070108 305373 305839 similar toUniRef100_A7PM30 Cluster: Chromosome chr14 scaffold_21, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape),partial (17%) AI461058 Glycine_(—) 305614 305834 NA max_release_(—) 2BE555571 Glycine_(—) 305656 306011 NA max_release_(—) 2 NGMAX008197032SEQ. 314847 315148 SEQ ID NO: 52 LISTING asmbl_11860 Vigna_(—) 319622320527 NA unguiculata EV270366 GMGI.071508 319893 320575 similar toUniRef100_P15792 Cluster: Protein kinase PVPK-1; n = 1; Phaseolusvulgaris|Rep: Protein kinase PVPK-1-Phaseolus vulgaris (Kidney bean)(French bean) = partial (34%) J04555 Phaseolus_(—) 318937 322709 Proteinkinase PVPK-1 vulgaris_(—) [Phaseolus vulgaris release_2 (Kidney bean)(French bean)] TA11578_34305 Lotus_(—) 320355 322024 Protein kinasePVPK-1 japonicus_(—) [Phaseolus vulgaris release_1 (Kidney bean) (Frenchbean)] TC35252 LJGI.070108 320355 322381 homologue to UniRef100_P15792Cluster: Protein kinase PVPK-1, n = 1, Phaseolus vulgaris|Rep: Proteinkinase PVPK-1 - Phaseolus vulgaris (Kidney bean) (French bean), partial(48%) Pvcon4227 Phaseolus_(—) 320098 322709 UniRef100_P15792 Proteinvulgaris kinase PVPK-1 n = 1 Tax = Phaseolus vulgaris RepID = KPK1_PHAVUE-0 CA900819 Phaseolus_(—) 325129 325547 Sucrase-like proteincoccineus_(—) [Arabidopsis thaliana release_2 (Mouse-ear cress)]CA900820 Phaseolus_(—) 325119 328122 AT3g27570/MMJ24_12 coccineus_(—)[Arabidopsis thaliana release_2 (Mouse-ear cress)] TC269193 GMGI.071508325136 329359 weakly similar to UniRef100_A7PM27 Cluster: Chromosomechr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitisvinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (47%) TA4354_3885Phaseolus_(—) 325476 329154 AT5g40510/MNF13_30 vulgaris_(—) [Arabidopsisthaliana release_2 (Mouse-ear cress)] asmbl_11861 Vigna_(—) 326881329154 NA unguiculata CF920945 Glycine_(—) 326967 329359AT3g27570/MMJ24_12 max_release_(—) [Arabidopsis thaliana 2 (Mouse-earcress)] SATT723 337605 337828 Satt723 ePCR 337605 337828 Map3.0 SSRL/Gm19 cM: 1.5 TC244213 GMGI.071508 354373 354996 similar toUniRef100_A7PL06 Cluster: Chromosome chr7 scaffold_20 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr7 scaffold_20= whole genome shotgun sequence - Vitis vinifera (Grape) = partial (17%)BU090380 Glycine_(—) 354683 354871 NA max_release_(—) 2 BP058294Lotus_(—) 355950 356319 Protein ycf2 [Lotus japonicus_(—) japonicus]release_1 Pvcon2444 Phaseolus_(—) 354593 360732 UniRef100_A7PL07vulgaris Chromosome chr7 scaffold_20, whole genome shotgun sequence n =1 Tax = Vitis vinifera RepID = A7PL07_VITVI 1.00E−144 asmbl_11862Vigna_(—) 359273 359896 NA unguiculata CA800649 Glycine_(—) 377994379933 AT3g01590/F4P13_13 max_release_(—) [Arabidopsis thaliana 2(Mouse-ear cress)] TC245493 GMGI.071508 377994 381638 similar toUniRef100_A7PM21 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (96%) CO984617 Glycine_(—) 379899 381537 At5g14500 [Arabidopsismax_release_(—) thaliana (Mouse-ear cress)] 2 M0114388 SEQ. 381308380486 SEQ ID NO: 8 LISTING AW704585 Glycine_(—) 381210 381673 At5g14500[Arabidopsis max_release_(—) thaliana (Mouse-ear cress)] 2 TC248588GMGI.071508 383419 383857 NA asmbl_11863 Vigna_(—) 383428 384088 NAunguiculata TC126554 MTGI.071708 383593 384668 weakly similar toUniRef100_Q940C3 Cluster: AT3g27530/MMJ24_7, n = 2, Arabidopsisthaliana|Rep: AT3g27530/MMJ24_7 - Arabidopsis thaliana (Mouse-earcress), partial (38%) AJ002216 Pisum_(—) 384088 384751 Emb|CAA07228.1sativum_(—) [Arabidopsis thaliana release_2 (Mouse-ear cress)] BI702257GMGI.071508 384067 384789 similar to UniRef100_Q940C3 Cluster:AT3g27530/MMJ24_7; n = 2; Arabidopsis thaliana|Rep: AT3g27530/MMJ24_7 -Arabidopsis thaliana (Mouse-ear cress) = partial (14%) BG451913MTGI.071708 386353 388007 similar to UniRef100_Q9LT59 Cluster:Emb|CAA07228.1, n = 1, Arabidopsis thaliana|Rep: Emb|CAA07228.1 -Arabidopsis thaliana (Mouse-ear cress), partial (19%) CV533025Phaseolus_(—) 388647 389345 UniRef100_UPI000016357 vulgaris E GC6(GOLGIN CANDIDATE 6) binding/ protein transporter Tax = n = 1 RepID =UPI000016357E 6.00E−27 AV777312 LJGI.070108 389152 391279 similar toUniRef100_Q9LT59 Cluster: Emb|CAA07228.1, n = 1, Arabidopsisthaliana|Rep: Emb|CAA07228.1 - Arabidopsis thaliana (Mouse-ear cress),partial (19%) BM187543 GMGI.071508 394984 395407 similar toUniRef100_A7PM13 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (36%) BM187543 Glycine_(—) 394984 395559 Gb|AAF01546.1max_release_(—) [Arabidopsis thaliana 2 [Mouse-ear cress)] DN652256LJGI.070108 395487 395708 similar to UniRef100_A7P4B1 Cluster:Chromosome chr1 scaffold_5, whole genome shotgun sequence, n = 1, Vitisvinifera|Rep: Chromosome chr1 scaffold_5, whole genome shotgunsequence - Vitis vinifera (Grape), partial (19%) DT044393 Arachis_(—)395462 395746 Cluster: Hypothetical hypogaea_(—) protein T23K23.27, n =1, release_5 Arabidopsis thaliana|Rep: Hypothetical protein T23K23.27 -Arabidopsis thaliana (Mouse-ear cress) FD789910 Phaseolus_(—) 395555395927 UniRef100_A7P4B1 vulgaris Chromosome chr1 scaffold_5, wholegenome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7P4B1_VITVI2.00E−59 EH259382 GMGI.071508 395577 396156 similar to UniRef100_A7PM13Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n= 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence - Vitis vinifera (Grape) = partial (34%) TA69305_3847Glycine_(—) 403237 404175 NA max_release_(—) 2 TC243910 GMGI.071508403237 404175 similar to UniRef100_A7PM14 Cluster: Chromosome chr14scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (5%) CA785084 Glycine_(—) 403526 404055 NAsoja_release_(—) 2 CV541170 Phaseolus_(—) 404688 406556 UniRef100_Q9LT57vulgaris_(—) Emb|CAB45506.1 n = 1 Tax = Arabidopsis thaliana RepID =Q9LT57_ARATH 1.00E−113 BF071095 GMGI.071508 406510 407127 similar toUniRef100_Q9LT57 Cluster: Emb|CAB45506.1; n = 1; Arabidopsisthaliana|Rep: Emb|CAB45506.1 - Arabidopsis thaliana (Mouse-ear cress) =partial (8%) BF071095 Glycine_(—) 406527 407127 NA max_release_(—) 2BM270669 Glycine_(—) 409910 410532 NA max_release_(—) 2 BM270669GMGI.071508 410045 410532 similar to UniRef100_A7PM16 Cluster:Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (9%) BG550673 GMGI.071508421541 422250 similar to UniRef100_A7PM12 Cluster: Chromosome chr14scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (26%) BG550673 Glycine_(—) 421541 422354Hypothetical protein max_release_(—) F18O22_260 [Arabidopsis 2 thaliana(Mouse-ear cress)] BU551363 Glycine_(—) 422150 422745 SEQ ID NO: 9max_release_(—) 2 CD407423 Glycine_(—) 423719 423842 NA max_release_(—)2 M0205350 SEQ 424095 423776 SEQ ID NO: 10 Listing EV270239 GMGI.071508425649 426181 similar to UniRef100_Q0WVR7 Cluster: TRNA synthase- likeprotein; n = 1; Arabidopsis thaliana|Rep: TRNA synthase-like protein -Arabidopsis thaliana (Mouse-ear cress) = partial (5%) BI424448GMGI.071508 451332 451679 similar to UniRef100_P82353 Cluster:Non-specific lipid- transfer protein 2; n = 1; Prunus armeniaca|Rep:Non-specific lipid-transfer protein 2 - Prunus armeniaca (Apricot) =partial (68%) TA49179_3847 Glycine_(—) 451332 451827 Nonspecificlipid-transfer max_release_(—) protein 2 [Prunus 2 armeniaca (Apricot)]TC252453 GMGI.071508 451397 451828 weakly similar to UniRef100_Q43681Cluster: Probable non- specific lipid-transfer protein AKCS9 precursor;n = 1; Vigna unguiculata|Rep: Probable non-specific lipid-transferprotein AKCS9 precursor - Vigna unguiculata (Cowpea) = partial (86%)BE609938 Glycine_(—) 451607 451756 Probable lipid transfermax_release_(—) protein family protein 2 [Tamarix androssowii] BQ612382Glycine_(—) 451777 452217 NA max_release_(—) 2 M0102027 466228 466889SEQ ID NO: 11 Pvcon7917 Phaseolus_(—) 466120 467338 UniRef100_A5C9E2vulgaris Putative uncharacterized protein n = 1 Tax = Vitis viniferaRepID = A5C9E2_VITVI 6.00E−44 asmbl_11864 Vigna_(—) 467520 468191 NAunguiculata TA49596_3847 Glycine_(—) 470086 472059 Methionineaminopeptidase max_release_(—) 2B [Arabidopsis thaliana 2 (Mouse-earcress)] TC255857 GMGI.071508 470086 476828 homologue to UniRef100_A7PXX3Cluster: Methionine aminopeptidase; n = 1; Vitis vinifera|Rep:Methionine aminopeptidase - Vitis vinifera (Grape) = partial (91%)FD792539 Phaseolus_(—) 472774 475674 UniRef100_A7PXX3 vulgarisMethionine aminopeptidase n = 1 Tax = Vitis vinifera RepID =A7PXX3_VITVI 5.00E−56 TA3829_3848 Glycine_(—) 471918 476623 Methionineaminopeptidase soja_release_(—) 2B [Arabidopsis thaliana 2 (Mouse-earcress)] BU765955 Glycine_(—) 472787 475846 Methionine max_release_(—)aminopeptidase 2B 2 [Arabidopsis thaliana (Mouse-ear cress)]. SEQ ID NO:12 EG530516 Arachis_(—) 472835 476690 Cluster: Methionine hypogaea_(—)aminopeptidase 2B, n = 1, release_5 Arabidopsis thaliana|Rep: Methionineaminopeptidase 2B - Arabidopsis thaliana (Mouse-ear cress) AV425234LJGI.070108 475562 475924 homologue to UniRef100_A7PXX3 Cluster:Methionine aminopeptidase, n = 1, Vitis vinifera|Rep: Methionineaminopeptidase - Vitis vinifera (Grape), partial (22%) TA49598_3847Glycine_(—) 474794 476709 Methionine aminopeptidase max_release_(—) 2B[Arabidopsis thaliana 2 (Mouse-ear cress)] FD797260 Phaseolus_(—) 475768476654 UniRef100_A7PXX3 vulgaris Methionine aminopeptidase n = 1 Tax =Vitis vinifera RepID = A7PXX3_VITVI 6.00E−55 BE823844 Glycine_(—) 475751476828 Methionine aminopeptidase max_release_(—) 2B [Arabidopsisthaliana 2 (Mouse-ear cress)] BG726070 Glycine_(—) 476668 476807 NAmax_release_(—) 2 BQ080926 GMGI.071508 480002 480636 similar toUniRef100_A7PY54 Cluster: Chromosome chr15 scaffold_37 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr15scaffold_37 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (39%) TA69442_3847 Glycine_(—) 480002 481069 Hypotheticalprotein max_release_(—) F22I13.40 [Arabidopsis 2 thaliana (Mouse-earcress)] TC262427 GMGI.071508 480002 481069 similar to UniRef100_A7P8Q6Cluster: Chromosome chr3 scaffold_8 = whole genome shotgun sequence; n =1; Vitis vinifera|Rep: Chromosome chr3 scaffold_8 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (20%) BU548976 Glycine_(—)481474 481970 Multi antimicrobial max_release_(—) extrusion protein MatE2 [Medicago truncatula (Barrel medic)] CX547082 Glycine_(—) 481345482173 Multi antimicrobial max_release_(—) extrusion protein MatE 2[Medicago truncatula (Barrel medic)] TC236122 GMGI.071508 481300 482612NA TA57759_3847 Glycine_(—) 481300 482627 Multi antimicrobialmax_release_(—) extrusion protein MatE 2 [Medicago truncatula (Barrelmedic)] AV420909 LJGI.070108 481846 482201 weakly similar toUniRef100_A7QTE8 Cluster: Chromosome undetermined scaffold_167, wholegenome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosomeundetermined scaffold_167, whole genome shotgun sequence - Vitisvinifera (Grape), partial (24%) AW597322 Glycine_(—) 481965 482825 Multiantimicrobial max_release_(—) extrusion protein MatE 2 [Medicagotruncatula (Barrel medic)] BM270610 Glycine_(—) 482034 483008 Multiantimicrobial max_release_(—) extrusion protein MatE 2 [Medicagotruncatula (Barrel medic)] BI972603 GMGI.071508 482632 483190 weaklysimilar to UniRef100_A7P3G6 Cluster: Chromosome chr1 scaffold_5 = wholegenome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr1scaffold_5 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (20%) BI972603 Glycine_(—) 482632 484113 Multi antimicrobialmax_release_(—) extrusion protein MatE 2 [Medicago truncatula (Barrelmedic)] TA66198_3847 Glycine_(—) 482595 484230 Multi antimicrobialmax_release_(—) extrusion protein MatE 2 [Medicago truncatula (Barrelmedic)] TC253566 GMGI.071508 482648 484405 weakly similar toUniRef100_A7QTE8 Cluster: Chromosome undetermined scaffold_167 = wholegenome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomeundetermined scaffold_167 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (44%) asmbl_11865 Vigna_(—) 482937 484289 NAunguiculata BG881371 Glycine_(—) 483075 484230 Multi antimicrobialmax_release_(—) extrusion protein MatE 2 [Medicago truncatula (Barrelmedic)] WmFPC_(—) 384071 598745 NA Contig7443 AW695419 MTGI.071708491367 494466 similar to UniRef100_A7PU69 Cluster: Chromosome chr7scaffold_31, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep:Chromosome chr7 scaffold_31, whole genome shotgun sequence - Vitisvinifera (Grape), partial (11%) BF645755 MTGI.071708 494870 497474similar to UniRef100_A7PU69 Cluster: Chromosome chr7 scaffold_31, wholegenome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr7scaffold_31, whole genome shotgun sequence - Vitis vinifera (Grape),partial (14%) BE475242 GMGI.071508 497000 497327 similar toUniRef100_A7NWE7 Cluster: Chromosome chr5 scaffold_2 whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: = partial (1%) BE475242Glycine_(—) 497000 497549 Hypothetical protein max_release_(—)At3g23590/MDB19_8 2 [Arabidopsis thaliana (Mouse-ear cress)] BW611072LJGI.070108 497387 497795 similar to UniRef100_A7PU69 Cluster:Chromosome chr7 scaffold_31, whole genome shotgun sequence, n = 1, Vitisvinifera|Rep: Chromosome chr7 scaffold_31, whole genome shotgunsequence - Vitis vinifera (Grape), partial (10%) BQ613050 Glycine_(—)497409 498014 ORF protein [Arabidopsis max_release_(—) thaliana(Mouse-ear cress)] 2 CV541244 Phaseolus_(—) 500143 500464UniRef100_A9PGX2 vulgaris Putative uncharacterized protein n = 1 Tax =Populus trichocarpa RepID = A9PGX2_POPTR 3.00E−28 CX856527 Glycine_(—)501517 501735 NA max_release_(—) 2 BG839076 Glycine_(—) 503126 505209F2P3.12 protein max_release_(—) [Arabidopsis thaliana 2 (Mouse-earcress)] FD790090 Phaseolus_(—) 503370 505191 No significant hit (e-20)vulgaris TC236383 GMGI.071508 503107 505675 similar to UniRef100_O82505Cluster: Elongation factor Ts; n = 1; Arabidopsis thaliana|Rep:Elongation factor Ts - Arabidopsis thaliana (Mouse-ear cress) = partial(32%) TA56246_3847 Glycine_(—) 503107 505848 Ethylene-responsivemax_release_(—) elongation factor EF-Ts 2 precursor [Lycopersiconesculentum (Tomato)] TC239475 GMGI.071508 503126 506560 similar toUniRef100_Q9SWW0 Cluster: Ethylene- responsive elongation factor EF-Tsprecursor; n = 1; Solanum lycopersicum|Rep: Ethylene-responsiveelongation factor EF-Ts precursor Solanum lycopersicum (Tomato)(Lycopersicon esculentum) = partial (74%) TA56245_3847 Glycine_(—)505512 506546 Ethylene-responsive max_release_(—) elongation factorEF-Ts 2 precursor [Lycopersicon esculentum (Tomato)] BG839060Glycine_(—) 505661 506530 At4g11120 [Arabidopsis max_release_(—)thaliana (Mouse-ear cress)] 2 CV543527 Phaseolus_(—) 508539 508771Eukaryotic translation vulgaris_(—) initiation factor 5 release_2[Phaseolus vulgaris (Kidney bean) (French bean)] CD393454 Glycine_(—)510651 511000 Ribosomal protein L22 max_release_(—) [Glycine max(Soybean)] 2 TC245517 GMGI.071508 510651 511270 homologue toUniRef100_O48879 Cluster: Ribosomal protein L22; n = 1; Glycine max|Rep:Ribosomal protein L22 - Glycine max (Soybean) = partial (80%)asmbl_11866 Vigna_(—) 510868 511269 NA unguiculata TA51206_3847Glycine_(—) 510702 512712 Ribosomal protein L22 max_release_(—) [Glycinemax (Soybean)] 2 TC249077 GMGI.071508 510771 512771 homologue toUniRef100_O48879 Cluster: Ribosomal protein L22; n = 1; Glycine max|Rep:Ribosomal protein L22 - Glycine max (Soybean) = partial (98%) BG316244Glycine_(—) 511015 512722 Ribosomal protein L22 max_release_(—) [Glycinemax (Soybean)] 2 BQ155270 MTGI.071708 513084 514936 similar toUniRef100_A7PR59 Cluster: Chromosome chr14 scaffold_26, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_26, whole genome shotgun sequence - Vitis vinifera (Grape),partial (52%) TC30151 LJGI.070108 514647 516395 similar toUniRef100_A7PR59 Cluster: Chromosome chr14 scaffold_26, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_26, whole genome shotgun sequence - Vitis vinifera (Grape),partial (29%) BP044357 Lotus_(—) 514647 516409 S-locus protein 8[Brassica japonicus_(—) campestris (Field mustard)] release_1 CB540591Phaseolus_(—) 514839 516355 No significant hit (e-20) vulgarisTA65114_3847 Glycine_(—) 523413 524053 At1g22990/F19G10_22max_release_(—) [Arabidopsis thaliana 2 (Mouse-ear cress)] TC259745GMGI.071508 523413 524067 similar to UniRef100_A7P3I8 Cluster:Chromosome chr1 scaffold_5 = whole genome shotgun sequence; n = 2; Vitisvinifera|Rep: Chromosome chr1 scaffold_5 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (56%) TA4332_47247 Lotus_(—)529321 530051 Actin-11 related cluster corniculatus_(—) release_1TA6031_34305 Lotus_(—) 529321 530051 Actin [Striga asiatica]japonicus_(—) release_1 TC32457 LJGI.070108 529321 530051 homologue toUniRef100_P30167 Cluster: Actin-58, n = 1, Solanum tuberosum|Rep:Actin-58 - Solanum tuberosum (Potato), partial (39%) AW351005Glycine_(—) 529380 530095 Actin [Striga asiatica] max_release_(—) 2TA43521_3847 Glycine_(—) 529306 530175 Actin-11 [Arabidopsismax_release_(—) thaliana (Mouse-ear cress)] 2 asmbl_11867 Vigna_(—)529342 530189 NA unguiculata AU240079 LJGI.070108 529747 530013homologue to UniRef100_P93372 Cluster: Actin-66, n = 1, Nicotianatabacum|Rep: Actin-66 - Nicotiana tabacum (Common tobacco), partial(25%) AU240079 Lotus_(—) 529747 530039 Actin-11 [Arabidopsisjaponicus_(—) thaliana (Mouse-ear cress)] release_1 EE127018 Arachis_(—)529933 530285 Cluster: Hypothetical hypogaea_(—) protein, n = 1, Oryzasativa release_5 (indica cultivar-group)|Rep: Hypothetical protein -Oryza sativa subsp. indica (Rice) TC240040 GMGI.071508 529306 531078homologue to UniRef100_P02581 Cluster: Actin-1; n = 1; Glycine max|Rep:Actin-1 - Glycine max (Soybean) = complete AW666288 Glycine_(—) 529980530789 Actin [Phaseolus acutifolius max_release_(—) (Tepary bean)] 2TA43509_3847 Glycine_(—) 529888 530911 Actin [Glycine maxmax_release_(—) (Soybean)] 2 TA6074_34305 Lotus_(—) 530031 531095Actin-1 [Sorghum bicolor japonicus_(—) (Sorghum) (Sorghum release_1vulgare)] TC26188 LJGI.070108 530031 531095 homologue toUniRef100_A1Y2A0 Cluster: Actin, n = 1, Aegiceras corniculatum|Rep:Actin - Aegiceras corniculatum, partial (81%) BM142797 Glycine_(—)530212 531095 Actin [Trifolium pratense max_release_(—) (Red clover)] 2BP036880 Lotus_(—) 530235 531095 Actin/actin-like [Medicagojaponicus_(—) truncatula (Barrel medic)] release_1 AW349632 Glycine_(—)533113 533701 NA max_release_(—) 2 AI900119 Glycine_(—) 533044 534995 NAmax_release_(—) 2 TA51800_3847 Glycine_(—) 533054 535063 NAmax_release_(—) 2 TC241826 GMGI.071508 533055 535063 similar toUniRef100_Q2Z1Y5 Cluster: Pm52 protein; n = 1; Prunus mume|Rep: Pm52protein - Prunus mume (Japanese flowering apricot) = partial (73%)BU494245 LJGI.070108 533191 534994 weakly similar to UniRef100_Q2Z1Y5Cluster: Pm52 protein, n = 1, Prunus mume|Rep: Pm52 protein - Prunusmume (Japanese flowering apricot), partial (59%) AI440735 Glycine_(—)534517 535020 NA max_release_(—) 2 AI440735 GMGI.071508 534522 535020similar to UniRef100_Q2Z1Y5 Cluster: Pm52 protein; n = 1; Prunusmume|Rep: Pm52 protein - Prunus mume (Japanese flowering apricot) =partial (41%) TC250013 GMGI.071508 536842 537680 UniRef100_Q8L7J4Cluster: Pyruvate kinase; n = 1; Glycine max|Rep: Pyruvate kinase -Glycine max (Soybean) = partial (29%) TA10574_34305 Lotus_(—) 537149537628 Pyruvate kinase [Glycine japonicus_(—) max (Soybean)] release_1TC26632 LJGI.070108 537149 537628 homologue to UniRef100_Q42806 Cluster:Pyruvate kinase, cytosolic isozyme, n = 1, Glycine max|Rep: Pyruvatekinase, cytosolic isozyme - Glycine max (Soybean), partial (26%)CV536725 Phaseolus_(—) 537147 537846 Pyruvate kinase = cytosolicvulgaris_(—) isozyme [Glycine max release_2 (Soybean)] asmbl_11868Vigna_(—) 537127 538325 NA unguiculata TC25282 LJGI.070108 537149 538489homologue to UniRef100_Q8L7J4 Cluster: Pyruvate kinase, n = 1, Glycinemax|Rep: Pyruvate kinase - Glycine max (Soybean), partial (29%)TA47094_3847 Glycine_(—) 536842 539314 Pyruvate kinase [Glycinemax_release_(—) max (Soybean)] 2 Pvcon4373 Phaseolus_(—) 537147 539113UniRef100_Q42806 vulgaris Pyruvate kinase, cytosolic isozyme n = 1 Tax =Glycine max RepID = KPYC_SOYBN E-0 TC124922 MTGI.071708 537491 538783homologue to UniRef100_Q42806 Cluster: Pyruvate kinase, cytosolicisozyme, n = 1, Glycine max|Rep: Pyruvate kinase, cytosolic isozyme -Glycine max (Soybean), partial (64%) BF598352 Glycine_(—) 538308 538971Pyruvate kinase [Citrus soja_release_(—) sinensis (Sweet orange)] 2BG044770 Glycine_(—) 538624 539149 Pyruvate kinase [Citrussoja_release_(—) sinensis (Sweet orange)] 2 TC249941 GMGI.071508 538549539314 UniRef100_Q8L7J4 Cluster: Pyruvate kinase; n = 1; Glycinemax|Rep: Pyruvate kinase - Glycine max (Soybean) = partial (37%)BE608312 Glycine_(—) 542536 544875 Hypothetical protein max_release_(—)[Arabidopsis thaliana 2 (Mouse-ear cress)] TC253996 GMGI.071508 542045546856 similar to UniRef100_A7QNQ5 Cluster: Chromosome undeterminedscaffold_133 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome undetermined scaffold_133 = whole genome shotgun sequence -Vitis vinifera (Grape) = partial (80%) TC258772 GMGI.071508 548268548805 NA CV533614 Phaseolus_(—) 548540 548638 No significant hitvulgaris TA57756_3847 Glycine_(—) 548268 551375 Putative microtubule-max_release_(—) severing protein subunit 2 [Oryza sativa (japonicacultivar-group)] TC239891 GMGI.071508 548323 551375 similar toUniRef100_A7QNQ6 Cluster: Chromosome undetermined scaffold_133 = wholegenome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomeundetermined scaffold_133 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (12%) EH221990 GMGI.071508 550796 551633weakly similar to UniRef100_A7QNQ6 Cluster: Chromosome undeterminedscaffold_133 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome undetermined scaffold_133 = whole genome shotgun sequence -Vitis vinifera (Grape) = partial (7%) EV263369 GMGI.071508 552842 553615similar to UniRef100_A8D2Q2 Cluster: ATP synthase protein 8; n = 1;Caranx ignobilis|Rep: ATP synthase protein 8 - Caranx ignobilis =partial (37%) BU964969 Glycine_(—) 556336 556943 NA max_release_(—) 2BU964969 GMGI.071508 556494 556943 similar to UniRef100_Q9MYM4 Cluster:Lysosomal alpha- glucosidase precursor; n = 1; Bos taurus|Rep: Lysosomalalpha-glucosidase = partial (1%) EH221989 GMGI.071508 562783 563692homologue to UniRef100_A7QNQ6 Cluster: Chromosome undeterminedscaffold_133 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome undetermined scaffold_133 = whole genome shotgun sequence -Vitis vinifera (Grape) = partial (3%) AW831441 GMGI.071508 573069 573567NA AW831441 Glycine_(—) 573069 573639 NA max_release_(—) 2 TA6761_34305Lotus_(—) 573706 580487 Sphingosine kinase [Lotus japonicus_(—)japonicus] release_1 TC20288 LJGI.070108 573706 580487 UniRef100_Q5KR50Cluster: Sphingosine kinase, n = 1, Lotus japonicus|Rep: Sphingosinekinase - Lotus japonicus, complete TC122322 MTGI.071708 574490 580620homologue to UniRef100_Q5KR50 Cluster: Sphingosine kinase, n = 1, Lotusjaponicus|Rep: Sphingosine kinase - Lotus japonicus, partial (66%)BI701010 Glycine_(—) 577145 579375 Sphingosine kinase [Lotusmax_release_(—) japonicus] 2 Pvcon3123 Phaseolus_(—) 577107 580468UniRef100_Q5KR50 vulgaris Sphingosine kinase n = 1 Tax = Lotus japonicusRepID = Q5KR50_LOTJA E-0 TA49258_3847 Glycine_(—) 579511 580791Sphingosine kinase [Lotus max_release_(—) japonicus] 2 TC235674GMGI.071508 579511 580791 homologue to UniRef100_Q5KR50 Cluster:Sphingosine kinase; n = 1; Lotus japonicus|Rep: Sphingosine kinase -Lotus japonicus = partial (26%) BI969866 Glycine_(—) 579600 580756Sphingosine kinase [Lotus max_release_(—) japonicus] 2 EH043869Arachis_(—) 579729 580660 Cluster: Sphingosine stenosperma_(—) kinase, n= 1, Lotus release_5 japonicus|Rep: Sphingosine kinase - Lotus japonicusBQ786742 Glycine_(—) 580594 580719 NA max_release_(—) 2 BM108235Glycine_(—) 581688 582006 NA max_release_(—) 2 AW508189 Glycine_(—)581725 582244 Hypothetical protein max_release_(—) [Arabidopsis thaliana2 (Mouse-ear cress)] TC238711 GMGI.071508 581688 582562 similar toUniRef100_A7QNQ7 Cluster: Chromosome undetermined scaffold_133 = wholegenome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomeundetermined scaffold_133 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (50%) TA46155_3847 Glycine_(—) 581745 582556Hypothetical protein max_release_(—) [Arabidopsis thaliana 2 (Mouse-earcress)] AW278369 GMGI.071508 581988 582389 similar to UniRef100_A7QNQ7Cluster: Chromosome undetermined scaffold_133 = whole genome shotgunsequence; n = 1; Vitis vinifera|Rep: Chromosome undeterminedscaffold_133 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (44%) AW278369 Glycine_(—) 581988 582418 Hypothetical proteinmax_release_(—) [Arabidopsis thaliana 2 (Mouse-ear cress)] CD394810Glycine_(—) 582134 582328 NA max_release_(—) 2 BG047332 Glycine_(—)591288 592013 OSJNBb0065L13.3 protein max_release_(—) [Oryza sativa(japonica 2 cultivar-group)] TC272805 GMGI.071508 591358 592013 similarto UniRef100_A7NXM8 Cluster: Chromosome chr5 scaffold_2 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr5 scaffold_2= whole genome shotgun sequence - Vitis vinifera (Grape) = partial (15%)BW599171 LJGI.070108 593399 593875 weakly similar to UniRef100_A7PT63Cluster: Chromosome chr8 scaffold_29, whole genome shotgun sequence, n =1, Vitis vinifera|Rep: Chromosome chr8 scaffold_29, whole genome shotgunsequence - Vitis vinifera (Grape), partial (24%) BE057829 Glycine_(—)606858 607008 NA max_release_(—) 2 TC275159 GMGI.071508 606858 607456 NABE612118 GMGI.071508 615853 616253 weakly similar to UniRef100_A7GPV4Cluster: Citrate transporter; n = 1; Bacillus cereus subsp. cytotoxisNVH 391-98|Rep: Citrate transporter - Bacillus cereus subsp. cytotoxis(strain NVH 391- 98) = partial (5%) BE612118 Glycine_(—) 615869 616269NA max_release_(—) 2 CA910895 Phaseolus_(—) 622174 622531 Arabidopsisthaliana coccineus_(—) genomic DNA, release_2 chromosome 5, P1 clone:MPO12 [Arabidopsis thaliana (Mouse-ear cress)] BU763992 Glycine_(—)625192 625591 NA max_release_(—) 2 TA51978_3847 Glycine_(—) 625330626304 Putative ethylene- max_release_(—) responsive protein [Oryza 2sativa (japonica cultivar- group)] TC236117 GMGI.071508 625330 626304similar to UniRef100_A7PM86 Cluster: Chromosome chr14 scaffold_21 =whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomechr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (43%) TC263881 GMGI.071508 625192 627651 similar toUniRef100_A7PM86 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (76%) TA51979_3847 Glycine_(—) 625252 627642 Putative ethyleneresponse max_release_(—) protein [Capsicum chinense 2 (Scotch bonnet)(Bonnet pepper)] TC236300 GMGI.071508 625318 627642 similar toUniRef100_A7PM86 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (98%) CA910548 Phaseolus_(—) 625559 627607 Putative ethyleneresponse coccineus_(—) protein [Capsicum chinense release_2 (Scotchbonnet) (Bonnet pepper)] Pvcon5808 Phaseolus_(—) 625567 627610UniRef100_A7PM86 vulgaris Chromosome chr14 scaffold_21, whole genomeshotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM86_VITVI2.00E−77 EV269595 GMGI.071508 627204 627569 similar to UniRef100_A7PM86Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n= 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence - Vitis vinifera (Grape) = partial (29%) BI273677Glycine_(—) 637550 637816 NA max_release_(—) 2 BP049107 Lotus_(—) 647584649419 Cinnamoyl CoA reductase- corniculatus_(—) like protein relatedcluster release_1 TC258382 GMGI.071508 646415 652371 weakly similar toUniRef100_A7PM88 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (72%) TA50222_3847 Glycine_(—) 646722 652222 Cinnamoyl CoAreductase- max_release_(—) like protein [Arabidopsis 2 thaliana(Mouse-ear cress)] SATT495 650288 650531 Satt495 ePCR 650288 650531Map3.0 SSR L/Gm19 cM: 2.7 AW099618 GMGI.071508 649276 652222 weaklysimilar to UniRef100_A7PM88 Cluster: Chromosome chr14 scaffold_21 =whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomechr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (23%) TA50296_3847 Glycine_(—) 674409 676421 NAmax_release_(—) 2 BQ629031 Glycine_(—) 674669 676494 NA max_release_(—)2 BM520842 Glycine_(—) 674685 676538 NA soja_release_(—) 2 TC264557GMGI.071508 674741 676494 NA BU765059 Glycine_(—) 674828 676698 NAmax_release_(—) 2 BU765059 GMGI.071508 674925 676698 weakly similar toUniRef100_A7L4B0 Cluster: Protein kinase; n = 1; Carica papaya|Rep:Protein kinase Carica papaya (Papaya) = partial (6%) TC264815GMGI.071508 674409 678111 weakly similar to UniRef100_A7L4B0 Cluster:Protein kinase; n = 1; Carica papaya|Rep: Protein kinase - Carica papaya(Papaya) = partial (14%) asmbl_11869 Vigna_(—) 676473 676672 NAunguiculata TA50295_3847 Glycine_(—) 674775 678957 NA max_release_(—) 2Pvcon1987 Phaseolus_(—) 674506 679702 UniRef100_A7L4B0 vulgaris Proteinkinase n = 1 Tax = Carica papaya RepID = A7L4B0_CARPA 1.00E−127 BM528477Glycine_(—) 676507 678111 NA max_release_(—) 2 TA11531_47247 Lotus_(—)676692 678714 Protein kinase-like protein corniculatus_(—) relatedcluster release_1 TA13031_34305 Lotus_(—) 676692 678714 Hypotheticalprotein japonicus_(—) At5g14720 [Arabidopsis release_1 thaliana(Mouse-ear cress)] TC31122 LJGI.070108 676701 678714 similar toUniRef100_A7L4B0 Cluster: Protein kinase, n = 1, Carica papaya|Rep:Protein kinase - Carica papaya (Papaya), partial (14%) TC255388GMGI.071508 679127 681361 homologue to UniRef100_A7PM90 Cluster:Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (44%) TC124284 MTGI.071708679117 681419 homologue to UniRef100_A7PM90 Cluster: Chromosome chr14scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep:Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitisvinifera (Grape), partial (48%) DV565290 Phaseolus_(—) 681368 681460 Nosignificant hit (e-20) vulgaris toGm05 DAGchainer 603011 803108 Ks0.2166NP7265365 MTGI.071708 703588 713159 GB|AC124951.19|ABE84834.1 ATPase,E1-E2 type, Peptidase M, neutral zinc metallopeptidases, zinc- bindingsite BF325038 Glycine_(—) 711165 712911 ATPase = E1-E2 type;max_release_(—) Peptidase M = neutral zinc 2 metallopeptidases = zinc-binding site [Medicago truncatula (Barrel medic)] FE897117 Phaseolus_(—)715539 715874 UniRef100_Q93VL6 NBS- vulgaris LRR resistance-like proteinJ78 n = 1 Tax = Phaseolus vulgaris RepID = Q93VL6_PHAVU 2.00E−47TC264844 GMGI.071508 731939 732440 weakly similar to UniRef100_A7PD05Cluster: Chromosome chr17 scaffold_12 = whole genome shotgun sequence; n= 1; Vitis vinifera|Rep: Chromosome chr17 scaffold_12 = whole genomeshotgun sequence - Vitis vinifera (Grape) = partial (13%) TA67235_3847Glycine_(—) 731939 733078 NA max_release_(—) 2 CD404253 GMGI.071508732439 733078 homologue to UniRef100_A7PM92 Cluster: Chromosome chr14scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (8%) BU091162 GMGI.071508 737876 738292 NABU091162 Glycine_(—) 737876 738363 NA max_release_(—) 2 asmbl_11870Vigna_(—) 740144 741401 NA unguiculata BI470779 GMGI.071508 740189741746 similar to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1;Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus(Mung bean) (Vigna radiata) = partial (30%) TA43150_3847 Glycine_(—)740126 742524 Carbonic anhydrase max_release_(—) [Phaseolus aureus(Mung2 bean) (Vigna radiata)] BG509786 GMGI.071508 740265 742434 homologue toUniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1; Vigna radiata var.radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vignaradiata) = partial (34%) BG509786 Glycine_(—) 740265 742656 Carbonicanhydrase [Zea max_release_(—) mays (Maize)] 2 DT083317 Glycine_(—)740299 742670 Carbonic anhydrase [Zea soja_release_(—) mays (Maize)] 2AW781596 Glycine_(—) 740182 742860 Carbonic anhydrase max_release_(—)[Phaseolus aureus (Mung 2 bean) (Vigna radiata)] BU089680 Glycine_(—)741070 742671 Carbonic anhydrase [Zea max_release_(—) mays (Maize)] 2BM887226 Glycine_(—) 741037 742852 Carbonic anhydrase [Zeamax_release_(—) mays (Maize)] 2 BU089600 Glycine_(—) 741070 742891Carbonic anhydrase [Zea max_release_(—) mays (Maize)] 2 TC23104LJGI.070108 740127 744319 similar to UniRef100_Q9XQB0 Cluster: Carbonicanhydrase, n = 1, Vigna radiata var. radiata|Rep: Carbonic anhydrase -Phaseolus aureus (Mung bean) (Vigna radiata), partial (98%) TA2934_3885Phaseolus_(—) 739932 744687 Carbonic anhydrase [Zea vulgaris_(—) mays(Maize)] release_2 TC238511 GMGI.071508 740118 744639 homologue toUniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1; Vigna radiata var.radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vignaradiata) = complete TA377_34305 Lotus_(—) 740127 744704 Carbonicanhydrase [Zea japonicus_(—) mays (Maize)] release_1 Pvcon229Phaseolus_(—) 740125 744728 UniRef100_Q9XQB0 vulgaris Carbonic anhydrasen = 1 Tax = Vigna radiata var. radiata RepID = Q9XQB0_PHAAU 1.00E−176TA2935_3885 Phaseolus_(—) 740178 744687 Carbonic anhydrase [Zeavulgaris_(—) mays (Maize)] release_2 TA2376_3848 Glycine_(—) 740118744805 Carbonic anhydrase soja_release_(—) [Phaseolus aureus (Mung 2bean) (Vigna radiata)] TA43157_3847 Glycine_(—) 740117 744844 Carbonicanhydrase [Zea max_release_(—) mays (Maize)] 2 TA43160_3847 Glycine_(—)741051 744186 Carbonic anhydrase = max_release_(—) chloroplast precursor(EC 2 4.2.1.1) (Carbonate dehydratase) [Contains: Carbonic anhydrase =27 kDa isoform; Carbonic anhydrase = 25 kDa isoform] [Pisum sativum(Garden pea)] TC135779 MTGI.071708 741364 744530 homologue toUniRef100_P17067 Cluster: Carbonic anhydrase, chloroplast precursor(Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform,Carbonic anhydrase, 25 kDa isoform], n = 1, Pisum sativum|Rep: Carbonicanhydrase, chloroplast precursor (Carbonate dehydratase) [Contains:Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDaisoform] - Pisum sativum (Garden pea), partial (79%) TA4174_3848Glycine_(—) 742624 743398 Carbonic anhydrase soja_release_(—) [Phaseolusaureus (Mung 2 bean) (Vigna radiata)] Pvcon228 Phaseolus_(—) 741374744687 UniRef100_Q9XQB0 vulgaris Carbonic anhydrase n = 1 Tax = Vignaradiata var. radiata RepID = Q9XQB0_PHAAU 1.00E−137 TA43163_3847Glycine_(—) 741381 744770 Carbonic anhydrase [Zea max_release_(—) mays(Maize)] 2 TC247359 GMGI.071508 741381 744770 homologue toUniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1; Vigna radiata var.radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vignaradiata) = partial (62%) BG045644 Glycine_(—) 742643 743622 Carbonicanhydrase = soja_release_(—) chloroplast precursor (EC 2 4.2.1.1)(Carbonate dehydratase) [Contains: Carbonic anhydrase = 27 kDa isoform;Carbonic anhydrase = 25 kDa isoform] [Pisum sativum (Garden pea)]Pvcon227 Phaseolus_(—) 741681 744687 UniRef100_Q9XQB0 vulgaris Carbonicanhydrase n = 1 Tax = Vigna radiata var. radiata RepID = Q9XQB0_PHAAU1.00E−133 TC124201 MTGI.071708 741922 744665 homologue toUniRef100_P17067 Cluster: Carbonic anhydrase, chloroplast precursor(Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform,Carbonic anhydrase, 25 kDa isoform], n = 1, Pisum sativum|Rep: Carbonicanhydrase, chloroplast precursor (Carbonate dehydratase) [Contains:Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDaisoform] - Pisum sativum (Garden pea), partial (57%) CB543710Phaseolus_(—) 742464 744532 Carbonic anhydrase vulgaris_(—) [Phaseolusaureus (Mung release_2 bean) (Vigna radiata)] CB539509 Phaseolus_(—)742480 744557 Carbonic anhydrase [Zea vulgaris_(—) mays (Maize)]release_2 TC126947 MTGI.071708 742434 744665 homologue toUniRef100_P17067 Cluster: Carbonic anhydrase, chloroplast precursor(Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform,Carbonic anhydrase, 25 kDa isoform], n = 1, Pisum sativum|Rep: Carbonicanhydrase, chloroplast precursor (Carbonate dehydratase) [Contains:Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDaisoform] - Pisum sativum (Garden pea), partial (51%) asmbl_11871Vigna_(—) 742823 744369 NA unguiculata asmbl_11872 Vigna_(—) 742628744687 NA unguiculata asmbl_11874 Vigna_(—) 742641 744687 NA unguiculataTA43165_3847 Glycine_(—) 742658 744772 Carbonic anhydrasemax_release_(—) [Phaseolus aureus (Mung 2 bean) (Vigna radiata)]TC241035 GMGI.071508 742658 744772 homologue to UniRef100_Q9XQB0Cluster: Carbonic anhydrase; n = 1; Vigna radiata var. radiata|Rep:Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata) =partial (38%) TA480_3888 Pisum_(—) 742823 744641 Carbonic anhydrase,sativum_(—) chloroplast precursor (EC release_2 4.2.1.1) (Carbonatedehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform, Carbonicanhydrase, 25 kDa isoform] [Pisum sativum (Garden pea)] TC240357GMGI.071508 742650 744828 homologue to UniRef100_Q9XQB0 Cluster:Carbonic anhydrase; n = 1; Vigna radiata var. radiata|Rep: Carbonicanhydrase - Phaseolus aureus (Mung bean) (Vigna radiata) = partial (38%)BE346766 Glycine_(—) 743636 744227 Carbonic anhydrase = max_release_(—)chloroplast precursor (EC 2 4.2.1.1) (Carbonate dehydratase) [Contains:Carbonic anhydrase = 27 kDa isoform; Carbonic anhydrase = 25 kDaisoform] [Pisum sativum (Garden pea)] AW596246 Glycine_(—) 743636 744243Carbonic anhydrase max_release_(—) [Phaseolus aureus (Mung 2 bean)(Vigna radiata)] BE807206 Glycine_(—) 743636 744244 Carbonic anhydrasemax_release_(—) [Phaseolus aureus (Mung 2 bean) (Vigna radiata)]CB280659 Phaseolus_(—) 743613 744419 Carbonic anhydrase vulgaris_(—)[Phaseolus aureus (Mung release_2 bean) (Vigna radiata)] asmbl_11875Vigna_(—) 743587 744642 NA unguiculata DT083076 Glycine_(—) 743565744678 Carbonic anhydrase soja_release_(—) [Phaseolus aureus (Mung 2bean) (Vigna radiata)] TC29040 LJGI.070108 743565 744702 similar toUniRef100_Q9XQB0 Cluster: Carbonic anhydrase, n = 1, Vigna radiata var.radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vignaradiata), partial (31%) TA134_47247 Lotus_(—) 743568 744704 Carbonicanhydrase related corniculatus_(—) cluster release_1 TA378_34305Lotus_(—) 743568 744704 Carbonic anhydrase, japonicus_(—) prokaryoticand plant release_1 [Medicago truncatula (Barrel medic)] TC24201LJGI.070108 743584 744704 similar to UniRef100_Q9XQB0 Cluster: Carbonicanhydrase, n = 1, Vigna radiata var. radiata|Rep: Carbonic anhydrase -Phaseolus aureus (Mung bean) (Vigna radiata), partial (25%) CB539196Phaseolus_(—) 743626 744687 Carbonic anhydrase vulgaris_(—) [Phaseolusaureus (Mung release_2 bean) (Vigna radiata)] AV413187 LJGI.070108744089 744647 similar to UniRef100_P27140 Cluster: Carbonic anhydrase,chloroplast precursor, n = 4, Arabidopsis thaliana|Rep: Carbonicanhydrase, chloroplast precursor - Arabidopsis thaliana (Mouse-earcress), partial (17%) AV413187 Lotus_(—) 744089 744672 Carbonicanhydrase, japonicus_(—) chloroplast precursor release_1 [Arabidopsisthaliana (Mouse-ear cress)] CD860850 Pisum_(—) 744145 744641 Carbonicanhydrase, sativum_(—) chloroplast precursor release_2 [Arabidopsisthaliana (Mouse-ear cress)] CD403834 Glycine_(—) 744076 744732 Carbonicanhydrase = max_release_(—) chloroplast precursor 2 [Arabidopsisthaliana (Mouse-ear cress)] CD415400 Glycine_(—) 744251 744691 NAmax_release_(—) 2 asmbl_11873 Vigna_(—) 744448 744649 NA unguiculataCB541850 Phaseolus_(—) 747218 747570 No significant hit (e-20) vulgarisBM953717 Glycine_(—) 747199 748912 Peptidase S1 and S6 = max_release_(—)chymotrypsin/Hap 2 [Medicago truncatula (Barrel medic)] EH256926GMGI.071508 747192 749279 homologue to UniRef100_A7Q7E6 Cluster:Chromosome chr18 scaffold_59 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr18 scaffold_59 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (21%) TA51716_3847Glycine_(—) 747191 749327 Putative DegP protease max_release_(—) [Oryzasativa (japonica 2 cultivar-group)] TC243148 GMGI.071508 747199 749327homologue to UniRef100_A7Q7E6 Cluster: Chromosome chr18 scaffold_59 =whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomechr18 scaffold_59 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (25%) AV768772 LJGI.070108 747281 749288 homologue toUniRef100_O22609 Cluster: Protease Do-like 1, chloroplast precursor, n =1, Arabidopsis thaliana|Rep: Protease Do-like 1, chloroplast precursor -Arabidopsis thaliana (Mouse-ear cress), partial (23%) BE807421Glycine_(—) 748776 749688 Peptidase S1 and S6 = max_release_(—)chymotrypsin/Hap 2 [Medicago truncatula (Barrel medic)] TA51715_3847Glycine_(—) 747251 752927 Peptidase S1 and S6 = max_release_(—)chymotrypsin/Hap 2 [Medicago truncatula (Barrel medic)] TC260884GMGI.071508 747251 752942 homologue to UniRef100_A7Q7E6 Cluster:Chromosome chr18 scaffold_59 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr18 scaffold_59 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (80%) BE474482 Glycine_(—)751068 752387 Peptidase S1 and S6 = max_release_(—) chymotrypsin/Hap 2[Medicago truncatula (Barrel medic)] BE474482 GMGI.071508 751070 752387homologue to UniRef100_A7Q7E6 Cluster: Chromosome chr18 scaffold_59 =whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomechr18 scaffold_59 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (19%) TC261290 GMGI.071508 755656 757218 similar toUniRef100_A7PM96 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (33%) BG646067 MTGI.071708 756996 759297 similar toUniRef100_A7PM96 Cluster: Chromosome chr14 scaffold_21, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape),partial (33%) BE555567 Glycine_(—) 757210 762134 Hypothetical proteinmax_release_(—) [Medicago truncatula 2 (Barrel medic)] BE555567GMGI.071508 757746 762134 similar to UniRef100_A7PM96 Cluster:Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (31%) BE058948 Glycine_(—)762117 763784 Hypothetical protein max_release_(—) [Medicago truncatula2 (Barrel medic)] BE058948 GMGI.071508 762818 763784 similar toUniRef100_A7PM96 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (25%) TC138874 MTGI.071708 768876 770881 similar toUniRef100_Q40318 Cluster: Coil protein, n = 1, Medicago sativa|Rep: Coilprotein - Medicago sativa (Alfalfa), partial (60%) TC124470 MTGI.071708768770 771318 similar to UniRef100_Q1RU40 Cluster: Lipolytic enzyme,G-D-S-L, n = 1, Medicago truncatula|Rep: Lipolytic enzyme, G-D-S-L -Medicago truncatula (Barrel medic), partial (77%) TC268582 GMGI.071508768733 771727 weakly similar to UniRef100_A7PMA0 Cluster: Chromosomechr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitisvinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (89%) BE059369 Glycine_(—)770328 771326 Lipolytic enzyme = G-D-S- max_release_(—) [Medicagotruncatula 2 (Barrel medic)] BE329784 GMGI.071508 770783 771236 similarto UniRef100_Q1RU40 Cluster: Lipolytic enzyme = G-D-S-L; n = 1; Medicagotruncatula|Rep: Lipolytic enzyme = G-D-S-L - Medicago truncatula (Barrelmedic) = partial (27%) BE329784 Glycine_(—) 770783 771288 Lipolyticenzyme = G-D-S- max_release_(—) L [Medicago truncatula 2 (Barrel medic)]TA68573_3847 Glycine_(—) 773983 774836 Putative kinesin light chainmax_release_(—) [Oryza sativa (japonica 2 cultivar-group)] TC259227GMGI.071508 773983 774836 similar to UniRef100_A7PD12 Cluster:Chromosome chr17 scaffold_12 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr17 scaffold_12 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (13%) AI759741 Glycine_(—)774118 774822 Putative kinesin light chain max_release_(—) [Oryza sativa(japonica 2 cultivar-group)] asmbl_11876 Vigna_(—) 774030 774978 NAunguiculata TC139308 MTGI.071708 774935 775598 similar toUniRef100_A7PMA1 Cluster: Chromosome chr14 scaffold_21, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape),partial (34%) AW186182 Glycine_(—) 775276 775796 Similarity to kinesinlight max_release_(—) chain [Arabidopsis thaliana 2 (Mouse-ear cress)]AW186182 GMGI.071508 775464 775796 similar to UniRef100_A7PD12 Cluster:Chromosome chr17 scaffold_12 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr17 scaffold_12 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (16%) BF010272 GMGI.071508783671 784035 UniRef100_Q00K67 Cluster: Major surface antigen; n = 1;Hepatitis B virus|Rep: Major surface antigen - Hepatitis B virus (HBV) =partial (5%) TA54422_3847 Glycine_(—) 783644 784982 Alcoholdehydrogenase max_release_(—) superfamily = zinc- 2 containing [Medicagotruncatula (Barrel medic)] BI971258 Glycine_(—) 783921 784926Auxin-induced protein max_release_(—) [Vigna radiata] 2 CV542673Phaseolus_(—) 784213 785346 Quinone oxidoreductase- vulgaris_(—) likeprotein [Helianthus release_2 annuus (Common sunflower)] TC239445GMGI.071508 783904 786356 similar to UniRef100_O23939 Cluster:Ripening-induced protein; n = 1; Fragaria vesca|Rep: Ripening- inducedprotein - Fragaria vesca (Woodland strawberry) = partial (84%)TA3037_3848 Glycine_(—) 784204 786191 Quinone oxidoreductase-soja_release_(—) like protein [Helianthus 2 annuus (Common sunflower)]BG045149 Glycine_(—) 784943 785469 Quinone oxidoreductasesoja_release_(—) [Fragaria ananassa 2 (Strawberry)] TA54423_3847Glycine_(—) 784420 786354 Quinone oxidoreductase- max_release_(—) likeprotein [Helianthus 2 annuus (Common sunflower)] BG046280 Glycine_(—)786163 786344 NA soja_release_(—) 2 CA901808 Phaseolus_(—) 800890 801759Alcohol dehydrogenase coccineus_(—) superfamily, zinc- release_2containing [Medicago truncatula (Barrel medic)] TA14086_34305 Lotus_(—)800932 801745 Alcohol dehydrogenase japonicus_(—) superfamily, zinc-release_1 containing [Medicago truncatula (Barrel medic)] TC23841LJGI.070108 800932 801745 similar to UniRef100_Q43677 Cluster:Auxin-induced protein, n = 1, Vigna radiata|Rep: Auxin-induced protein -Vigna radiata, partial (40%) M0093116 SEQ. 805373 805788 SEQ ID NO: 13Listing TC252650 GMGI.071508 805357 806601 similar to UniRef100_Q43677Cluster: Auxin-induced protein; n = 1; Vigna radiata|Rep: Auxin-inducedprotein - Vigna radiata = partial (54%) BARC-039375- ePCR&blat 805660806532 Map3.0 SNP L/Gm19 cM: 07304 3.4 TA65006_3847 Glycine_(—) 805357807089 Quinone oxidoreductase- max_release_(—) like protein [Helianthus2 annuus (Common sunflower)] TA65005_3847 Glycine_(—) 806611 807310Alcohol dehydrogenase max_release_(—) superfamily = zinc- 2 containing[Medicago truncatula (Barrel medic)] TC274718 GMGI.071508 806611 807310similar to UniRef100_Q43677 Cluster: Auxin-induced protein; n = 1; Vignaradiata|Rep: Auxin-induced protein - Vigna radiata = partial (30%)AW397551 Glycine_(—) 811245 811796 Auxin-induced protein max_release_(—)[Vigna radiata] 2 Pvcon4580 Phaseolus_(—) 811330 813524 UniRef100_Q43677Auxin- vulgaris induced protein n = 1 Tax = Vigna radiata RepID =Q43677_9FABA 1.00E−133 asmbl_11877 Vigna_(—) 812523 812779 NAunguiculata BE608172 Glycine_(—) 821487 822389 Proteinfarnesyltransferase max_release_(—) subunit beta [Pisum 2 sativum(Garden pea)] BQ273477 Glycine_(—) 821559 822383 NA max_release_(—) 2TC246895 GMGI.071508 821516 822443 similar to UniRef100_Q04903 Cluster:Protein farnesyltransferase subunit beta; n = 1; Pisum sativum|Rep:Protein farnesyltransferase subunit beta - Pisum sativum (Garden pea) =partial (15%) TC241767 GMGI.071508 824186 828116 similar toUniRef100_Q7XHJ0 Cluster: Formate dehydrogenase; n = 1; Quercusrobur|Rep: Formate dehydrogenase - Quercus robur (English oak) = partial(97%) TA40711_3847 Glycine_(—) 824209 828372 Formate dehydrogenasemax_release_(—) [Quercus robur (English 2 oak)] AI522957 Glycine_(—)826883 827087 Formate dehydrogenase max_release_(—) [Quercus robur(English 2 oak)] BG044450 Glycine_(—) 826544 827461 Formatedehydrogenase = soja_release_(—) mitochondrial precursor 2 [Solanumtuberosum (Potato)] asmbl_11878 Vigna_(—) 826586 827463 NA unguiculataCA800817 Glycine_(—) 826705 827869 Formate dehydrogenasesoja_release_(—) [Quercus robur (English 2 oak)] TC240429 GMGI.071508826957 828379 similar to UniRef100_Q9ZRI8 Cluster: Formate dehydrogenase= mitochondrial precursor; n = 1; Hordeum vulgare|Rep: Formatedehydrogenase = mitochondrial precursor - Hordeum vulgare (Barley) =partial (40%) AW350528 Glycine_(—) 826986 828379 Formate dehydrogenase 1= max_release_(—) mitochondrial precursor 2 [Oryza sativa (Rice)]BG882062 Glycine_(—) 827372 828284 Formate dehydrogenase 1 =max_release_(—) mitochondrial precursor 2 [Oryza sativa (Rice)] BE347639Glycine_(—) 827443 828262 Formate dehydrogenase 1 = max_release_(—)mitochondrial precursor 2 [Oryza sativa (Rice)] CA782711 Glycine_(—)827371 828357 Formate dehydrogenase 1 = soja_release_(—) mitochondrialprecursor 2 [Oryza sativa (Rice)] TA40821_3847 Glycine_(—) 829640 832253Formate dehydrogenase max_release_(—) [Quercus robur (English 2 oak)]BE330555 Glycine_(—) 829875 832057 Formate dehydrogenase =max_release_(—) mitochondrial precursor 2 [Solanum tuberosum (Potato)]BU090495 Glycine_(—) 829863 832082 Formate dehydrogenase max_release_(—)[Quercus robur (English 2 oak)] BG044406 Glycine_(—) 829915 832082Formate dehydrogenase soja_release_(—) [Quercus robur (English 2 oak)]AW508186 GMGI.071508 830914 831336 similar to UniRef100_A7PMA5 Cluster:Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (15%) M0129925 SEQ 830552831704 SEQ ID NO: 14 LISTING AW508186 Glycine_(—) 830914 831970 Formatedehydrogenase = max_release_(—) mitochondrial precursor 2 [Solatiumtuberosum (Potato)] AW508145 Glycine_(—) 830909 832061 Formatedehydrogenase max_release_(—) [Quercus robur (English 2 oak)]TA40373_3847 Glycine_(—) 830863 832118 Formate dehydrogenasemax_release_(—) [Quercus robur (English 2 oak)] AW397259 Glycine_(—)831219 832141 Formate dehydrogenase max_release_(—) [Quercus robur(English 2 oak)] TC261330 GMGI.071508 829795 833576 similar toUniRef100_Q7XHJ0 Cluster: Formate dehydrogenase; n = 1; Quercusrobur|Rep: Formate dehydrogenase - Quercus robur (English oak) = partial(96%) TC249502 GMGI.071508 830866 832529 similar to UniRef100_Q7XHJ0Cluster: Formate dehydrogenase; n = 1; Quercus robur|Rep: Formatedehydrogenase - Quercus robur (English oak) = partial (72%) TA40376_3847Glycine_(—) 830879 833356 Formate dehydrogenase max_release_(—) [Quercusrobur (English 2 oak)] asmbl_11879 Vigna_(—) 831735 833050 NAunguiculata AW569072 GMGI.071508 832471 832890 similar toUniRef100_Q7XHJ0 Cluster: Formate dehydrogenase; n = 1; Quercusrobur|Rep: Formate dehydrogenase - Quercus robur (English oak) = partial(9%) AW569072 Glycine_(—) 832471 832929 Formate dehydrogenasemax_release_(—) [Quercus robur (English 2 oak)] TA40339_3847 Glycine_(—)832130 833531 Formate dehydrogenase 1 = max_release_(—) mitochondrialprecursor 2 [Oryza sativa (Rice)] TA5191_3885 Phaseolus_(—) 832192833517 Formate dehydrogenase vulgaris_(—) [Quercus robur (Englishrelease_2 oak)] FD790937 Phaseolus_(—) 833039 833412 UniRef100_A6N0B2vulgaris Mitochondrial formate dehydrogenase 1 (Fragment) n = 1 Tax =Oryza sativa Indica Group RepID = A6N0B2_ORYSI 3.00E−30 CA913454Phaseolus_(—) 841331 841722 NA coccineus_(—) release_2 TA70199_3847Glycine_(—) 841305 841824 NA max_release_(—) 2 asmbl_11880 Vigna_(—)841326 841889 NA unguiculata TA3611_3848 Glycine_(—) 841347 842640Hypothetical protein soja_release_(—) OJ1593_C11.11 [Oryza 2 sativa(japonica cultivar- group)] TA5381_34305 Lotus_(—) 841455 842700 Calciumhomeostasis japonicus_(—) regulator CHoR1 [Solanum release_1 tuberosum(Potato)] TC20706 LJGI.070108 841455 842700 weakly similar toUniRef100_Q5QTN8 Cluster: Calcium homeostasis regulator CHoR1, n = 1,Solanum tuberosum|Rep: Calcium homeostasis regulator CHoR1 - Solanumtuberosum (Potato), partial (52%) Pvcon2378 Phaseolus_(—) 841347 843522UniRef100_A7PMA9 vulgaris Chromosome chr14 scaffold_21, whole genomeshotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMA9_VITVI4.00E−94 TC252755 GMGI.071508 841305 843655 similar to UniRef100_A7PMA9Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n= 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence - Vitis vinifera (Grape) = partial (74%) EX305183Phaseolus_(—) 841682 843613 UniRef100_A7PMA9 vulgaris Chromosome chr14scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis viniferaRepID = A7PMA9_VITVI 1.00E−67 BI498351 GMGI.071508 844582 845168 NATA66563_3847 Glycine_(—) 844582 847078 Hypothetical proteinmax_release_(—) [Ipomoea trifida (Morning 2 glory)] TC247953 GMGI.071508844582 847220 similar to UniRef100_A7Q5T8 Cluster: Chromosome chr14scaffold_54 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome chr14 scaffold_54 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (58%) TA3593_3848 Glycine_(—) 844668 847194Hypothetical protein soja_release_(—) [Ipomoea trifida (Morning 2glory)] TA56324_3847 Glycine_(—) 854425 856413 Similarity tointracellular max_release_(—) protein [Arabidopsis 2 thaliana (Mouse-earcress)] TC235843 GMGI.071508 854425 856413 similar to UniRef100_A7PMB1Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n= 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence - Vitis vinifera (Grape) = partial (40%) CD406351Glycine_(—) 855627 856402 Similarity to intracellular max_release_(—)protein [Arabidopsis 2 thaliana (Mouse-ear cress)] TC276442 GMGI.071508855627 856402 similar to UniRef100_A7PMB1 Cluster: Chromosome chr14scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (14%) TC273993 GMGI.071508 863632 864262homologue to UniRef100_A7PMB2 Cluster: Chromosome chr14 scaffold_21 =whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomechr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (26%) BU082700 Glycine_(—) 863841 864449 Hypotheticalprotein max_release_(—) OJ1126_B10.9 [Oryza 2 sativa (japonica cultivar-group)] AW459960 Glycine_(—) 863632 865288 Hypothetical proteinmax_release_(—) F4P13.4 [Arabidopsis 2 thaliana (Mouse-ear cress)]AL385435 MTGI.071708 863952 865397 homologue to UniRef100_A7PD25Cluster: Chromosome chr17 scaffold_12, whole genome shotgun sequence, n= 1, Vitis vinifera|Rep: Chromosome chr17 scaffold_12, whole genomeshotgun sequence - Vitis vinifera (Grape), partial (37%) AI856244GMGI.071508 864500 864958 UniRef100_A7PMB2 Cluster: Chromosome chr14scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (6%) asmbl_11881 Vigna_(—) 863829 865710 NAunguiculata TC238318 GMGI.071508 863970 865869 homologue toUniRef100_A7PMB2 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (34%) TA63907_3847 Glycine_(—) 864500 865869 Hypotheticalprotein max_release_(—) F4P13.4 [Arabidopsis 2 thaliana (Mouse-earcress)] BW598574 LJGI.070108 865265 865656 similar to UniRef100_Q8LES3Cluster: Protein kinase, n = 1, Arabidopsis thaliana|Rep: Proteinkinase - Arabidopsis thaliana (Mouse-ear cress), partial (9%) BW598574Lotus_(—) 865265 865674 Protein kinase [Arabidopsis japonicus_(—)thaliana (Mouse-ear cress)] release_1 CD400016 Glycine_(—) 870972 871184NA max_release_(—) 2 CD399245 Glycine_(—) 870876 871427 PutativePeptidyl-prolyl cis- max_release_(—) trans isomerase = 2 chloroplast[Oryza sativa (japonica cultivar-group)] TC242592 GMGI.071508 870943872827 similar to UniRef100_A6MZC4 Cluster: Peptidyl-prolyl cis- transisomerase; n = 2; Oryza sativa|Rep: Peptidyl-prolyl cis-transisomerase - Oryza sativa subsp. indica (Rice) = partial (60%) CB543642Phaseolus_(—) 871229 872777 Peptidyl-prolyl cis-trans vulgaris_(—)isomerase = chloroplast release_2 precursor [Spinacia oleracea(Spinach)] TA52959_3847 Glycine_(—) 870943 873450 Poly(A) polymerase[Pisum max_release_(—) sativum (Garden pea)] 2 CB539263 Phaseolus_(—)871195 873325 Poly(A) polymerase [Pisum vulgaris_(—) sativum (Gardenpea)] release_2 Pvcon1578 Phaseolus_(—) 870946 876143 UniRef100_O22636vulgaris Poly(A) polymerase n = 1 Tax = Pisum sativum RepID = O22636_PEAE-0 TA10487_34305 Lotus_(—) 873266 875963 Poly(A) polymerase [Pisumjaponicus_(—) sativum (Garden pea)] release_1 TA6667_47247 Lotus_(—)873266 875963 Poly(A) polymerase related corniculatus_(—) clusterrelease_1 TC34747 LJGI.070108 873266 875963 similar to UniRef100_O22636Cluster: Poly(A) polymerase, n = 1, Pisum sativum|Rep: Poly(A)polymerase - Pisum sativum (Garden pea), partial (57%) BG363373Glycine_(—) 874357 874944 Poly(A) polymerase [Pisum max_release_(—)sativum (Garden pea)] 2 TC251420 GMGI.071508 874369 876078 similar toUniRef100_O22636 Cluster: Poly(A) polymerase; n = 1; Pisum sativum|Rep:Poly(A) polymerase - Pisum sativum (Garden pea) = partial (37%) CA901088Phaseolus_(—) 874490 876191 Poly(A) polymerase [Pisum coccineus_(—)sativum (Garden pea)] release_2 asmbl_11882 Vigna_(—) 886629 890018 NAunguiculata TA68870_3847 Glycine_(—) 886534 893419 Senescence-associatedmax_release_(—) protein-like [Oryza sativa 2 (japonica cultivar-group)]TC270337 GMGI.071508 886672 893419 weakly similar to UniRef100_A7PD28Cluster: Chromosome chr17 scaffold_12 = whole genome shotgun sequence; n= 1; Vitis vinifera|Rep: Chromosome chr17 scaffold_12 = whole genomeshotgun sequence - Vitis vinifera (Grape) = partial (86%) M0205537 SEQ.890458 890051 SEQ ID NO: 15 Listing BM732054 Glycine_(—) 899859 901015NA max_release_(—) 2 BM732054 GMGI.071508 900006 901015 similar toUniRef100_Q04TD2 Cluster: MviN-related protein; n = 1; Leptospiraborgpetersenii serovar Hardjo-bovis JB197|Rep: = partial (2%) toGm13DAGchainer 816170 1014875 Ks0.1202 M0202715 SEQ. 921233 921630 SEQ IDNO: 16 Listing TA46168_3847 Glycine_(—) 921047 924660 Homeodomainleucine max_release_(—) zipper protein HDZ3 2 [Phaseolus vulgaris(Kidney bean) (French bean)] TC260016 GMGI.071508 921056 924739homologue to UniRef100_Q93XA3 Cluster: Homeodomain leucine zipperprotein HDZ3; n = 1; Phaseolus vulgaris|Rep: Homeodomain leucine zipperprotein HDZ3 - Phaseolus vulgaris (Kidney bean) (French bean) = completePvcon1101 Phaseolus_(—) 921086 924758 UniRef100_Q93XA3 vulgarisHomeodomain leucine zipper protein HDZ3 (Fragment) n = 1 Tax = Phaseolusvulgaris RepID = Q93XA3_PHAVU 1.00E−124 TA3604_3885 Phaseolus_(—) 921111924754 Homeodomain leucine vulgaris_(—) zipper protein HDZ3 release_2[Phaseolus vulgaris (Kidney bean) (French bean)] asmbl_11883 Vigna_(—)921538 924758 NA unguiculata BG041631 Glycine_(—) 923015 923340Homeobox-leucine zipper soja_release_(—) protein HAT5 [Arabidopsis 2thaliana (Mouse-ear cress)] AV421688 LJGI.070108 923118 924180 similarto UniRef100_Q93XA3 Cluster: Homeodomain leucine zipper protein HDZ3, n= 1, Phaseolus vulgaris|Rep: Homeodomain leucine zipper protein HDZ3 -Phaseolus vulgaris (Kidney bean) (French bean), partial (25%) TC235979GMGI.071508 923000 924768 similar to UniRef100_Q93XA3 Cluster:Homeodomain leucine zipper protein HDZ3; n = 1; Phaseolus vulgaris|Rep:Homeodomain leucine zipper protein HDZ3 - Phaseolus vulgaris (Kidneybean) (French bean) = partial (86%) TA46165_3847 Glycine_(—) 923000924779 Homeodomain leucine max_release_(—) zipper protein HDZ3 2[Phaseolus vulgaris (Kidney bean) (French bean)] AW351287 Glycine_(—)923128 924720 Homeodomain leucine max_release_(—) zipper protein HDZ3 2[Phaseolus vulgaris (Kidney bean) (French bean)] CA785782 Glycine_(—)925713 925880 NA soja_release_(—) 2 Pvcon8364 Phaseolus_(—) 925735926609 UniRef100_A7PMB7 vulgaris Chromosome chr14 scaffold_21, wholegenome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMB7_VITVI1.00E−27 BE248998 MTGI.071708 926978 927524 similar to UniRef100_Q7F8S7Cluster: PHD finger-like protein, n = 1, Oryza sativa JaponicaGroup|Rep: PHD finger-like protein - Oryza sativa subsp. japonica(Rice), partial (4%) TC35470 LJGI.070108 928423 929804 similar toUniRef100_A7PMB8 Cluster: Chromosome chr14 scaffold_21, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape),partial (9%) TA11035_34305 Lotus_(—) 928423 929825 PHD finger-likeprotein japonicus_(—) [Oryza sativa (japonica release_1 cultivar-group)]CA911004 Phaseolus_(—) 934882 939256 T13O15.10 protein coccineus_(—)[Arabidopsis thaliana release_2 (Mouse-ear cress)] AI856399 GMGI.071508937577 938041 NA AI856399 Glycine_(—) 937577 938106 NA max_release_(—) 2AW348703 Glycine_(—) 963043 963750 NA max_release_(—) 2 TC276191GMGI.071508 963049 964044 weakly similar to UniRef100_A7PZY3 Cluster:Chromosome chr8 scaffold_41 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr8 scaffold_41 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (21%) BQ628183 Glycine_(—)963625 964044 NA max_release_(—) 2 BQ080193 Glycine_(—) 963695 967475 NAmax_release_(—) 2 TA52645_3847 Glycine_(—) 963720 967461 NAmax_release_(—) 2 TC256882 GMGI.071508 963774 967475 weakly similar toUniRef100_A7PZY3 Cluster: Chromosome chr8 scaffold_41 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr8 scaffold_41= whole genome shotgun sequence - Vitis vinifera (Grape) = partial (45%)BG156825 Glycine_(—) 971121 971284 NA max_release_(—) 2 BG156825GMGI.071508 971125 971284 NA BU545761 Glycine_(—) 971300 971901 NAmax_release_(—) 2 BU550718 Glycine_(—) 971255 973578 NA max_release_(—)2 TA72701_3847 Glycine_(—) 972120 972806 NA max_release_(—) 2 TC271942GMGI.071508 972201 972806 NA TC269989 GMGI.071508 971255 973827 similarto UniRef100_A7P2M9 Cluster: Chromosome chr1 scaffold_5 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr1 scaffold_5= whole genome shotgun sequence - Vitis vinifera (Grape) = partial (63%)BI317782 Glycine_(—) 971510 973827 NA max_release_(—) 2 BI893512Glycine_(—) 971537 973848 NA max_release_(—) 2 BI893512 GMGI.071508971671 973848 similar to UniRef100_A7P2M9 Cluster: Chromosome chr1scaffold_5 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep:Chromosome chr1 scaffold_5 = whole genome shotgun sequence - Vitisvinifera (Grape) = partial (54%) CO985587 Glycine_(—) 974859 976255Putative GTP-binding max_release_(—) membrane protein LepA 2 [Oryzasativa (japonica cultivar-group)] AW596868 Glycine_(—) 976346 976856 NAmax_release_(—) 2 AW596868 GMGI.071508 976412 976856 similar toUniRef100_A2Q5T1 Cluster: Tetratricopeptide- like helical; n = 1;Medicago truncatula|Rep: Tetratricopeptide-like helical - Medicagotruncatula (Barrel medic) = partial (5%) CA901672 Phaseolus_(—) 983905984264 Aldehyde dehydrogenase 1 coccineus_(—) precursor [Lotus release_2corniculatus (Bird's-foot trefoil) WmFPC_(—) 899736 1068750 NAContig4169 FE898889 Phaseolus_(—) 983908 984989 UniRef100_A7PD33vulgaris Chromosome chr17 scaffold_12, whole genome shotgun sequence n =1 Tax = Vitis vinifera RepID = A7PD33_VITVI 2.00E−79 TC273361GMGI.071508 984396 986122 similar to UniRef100_P93344 Cluster: Aldehydedehydrogenase; n = 1; Nicotiana tabacum|Rep: Aldehyde dehydrogenase -Nicotiana tabacum (Common tobacco) = partial (37%) BE473475 Glycine_(—)984960 986122 Aldehyde dehydrogenase max_release_(—) [Nicotiana tabacum2 (Common tobacco)] CV539672 Phaseolus_(—) 985959 987101UniRef100_P93344 vulgaris Aldehyde dehydrogenase (NAD+) n = 1 Tax =Nicotiana tabacum RepID = P93344_TOBAC 7.00E−50 AV410805 LJGI.070108987592 987888 similar to UniRef100_A7PMC7 Cluster: Chromosome chr14scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep:Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitisvinifera (Grape), partial (6%) TC265505 GMGI.071508 1011306 1012664similar to UniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21 =whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomechr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (28%) TA51641_3847 Glycine_(—) 1011306 1013783Putative high-affinity max_release_(—) potassium transporter 2 protein 1[Nicotiana tabacum (Common tobacco)] CB540416 Phaseolus_(—) 10123331013531 UniRef100_A7PMD1 vulgaris Chromosome chr14 scaffold_21, wholegenome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMD1_VITVI5.00E−97 BM891067 GMGI.071508 1012675 1013617 similar toUniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (22%) TC131883 MTGI.071708 1012665 1014070 similar toUniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21, whole genomeshotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape),partial (34%) asmbl_11884 Vigna_(—) 1012674 1014123 NA unguiculataBE330787 Glycine_(—) 1013888 1014305 Putative high-affinitymax_release_(—) potassium transporter 2 protein [Phytolacca esculenta(Food pokeberry)] FD792954 Phaseolus_(—) 1013779 1014573UniRef100_A7PMD1 vulgaris Chromosome chr14 scaffold_21, whole genomeshotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMD1_VITVI3.00E−57 TC244134 GMGI.071508 1014004 1014793 similar toUniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (15%) TA51642_3847 Glycine_(—) 1013926 1014875 Putativehigh-affinity max_release_(—) potassium transporter 1 2 [Nicotianarustica (Aztec tobacco)] TC242106 GMGI.071508 1013926 1014875 similar toUniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (15%) BI970123 Glycine_(—) 1014128 1014721 Putative potassiummax_release_(—) transporter HAK1p 2 [Mesembryanthemum crystallinum(Common ice plant)] BQ080303 Glycine_(—) 1018604 1019142 NAmax_release_(—) 2 TC270109 GMGI.071508 1018604 1019142 weakly similar toUniRef100_UPI0000196D3 9 Cluster: NHL repeat- containing protein; n = 1;Arabidopsis thaliana|Rep: NHL repeat-containing protein - Arabidopsisthaliana = partial (4%) BQ080219 Glycine_(—) 1018604 1019579 NAmax_release_(—) 2 TA62145_3847 Glycine_(—) 1021347 1023221 NAmax_release_(—) 2 TC245123 GMGI.071508 1021347 1023221 similar toUniRef100_A7PMD2 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (31%) asmbl_11885 Vigna_(—) 1022417 1022510 NA unguiculataCA784724 Glycine_(—) 1046117 1047384 NA max_release_(—) 2 CA784724GMGI.071508 1046400 1047384 similar to UniRef100_A7Q2E7 Cluster:Chromosome chr1 scaffold_46 = whole genome shotgun sequence; n = 1;Vitis vinifera|Rep: Chromosome chr1 scaffold_46 = whole genome shotgunsequence - Vitis vinifera (Grape) = partial (17%) Pvcon4015Phaseolus_(—) 1047011 1048610 UniRef100_A5ATC1 vulgaris Putativeuncharacterized protein n = 1 Tax = Vitis vinifera RepID = A5ATC1_VITVI1.00E−146 BQ742289 Glycine_(—) 1048650 1048767 NA max_release_(—) 2BF068315 GMGI.071508 1057203 1057316 similar to UniRef100_Q8MIG1Cluster: Skinkine; n = 1; Sus scrofa|Rep: Skinkine - Sus scrofa (Pig) =partial (12%) BF068315 Glycine_(—) 1057203 1057506 NA max_release_(—) 2BU083500 GMGI.071508 1058026 1058431 UniRef100_Q2R023 Cluster: Expressedprotein; n = 1; Oryza sativa Japonica Group|Rep: Expressed protein -Oryza sativa = partial (2%) TA74227_3847 Glycine_(—) 1058026 1059408 NAmax_release_(—) 2 BI423963 GMGI.071508 1058432 1059275 similar toUniRef100_Q2QDD6 Cluster: Nodulin-like protein; n = 1; Gossypiumhirsutum|Rep: Nodulin-like protein - Gossypium hirsutum (Upland cotton)(Gossypium mexicanum) = partial (22%) TC237120 GMGI.071508 10630151063972 UniRef100_Q39819 Cluster: Hsp22.3; n = 1; Glycine max|Rep:Hsp22.3 - Glycine max (Soybean) = complete CA802234 Glycine_(—) 10614771067499 Similarity to nodulin soja_release_(—) [Arabidopsis thaliana 2(Mouse-ear cress)] BI425574 GMGI.071508 1065519 1066854 weakly similarto UniRef100_A7PMD8 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (21%) BI425574 Glycine_(—) 1065519 1066940 Hypothetical proteinmax_release_(—) [Medicago truncatula 2 (Barrel medic)] AU251786LJGI.070108 1066790 1067424 weakly similar to UniRef100_A7Q2G7 Cluster:Chromosome chr1 scaffold_46, whole genome shotgun sequence, n = 1, Vitisvinifera|Rep: Chromosome chr1 scaffold_46, whole genome shotgunsequence - Vitis vinifera (Grape), partial (7%) Pvcon8451 Phaseolus_(—)1065511 1068752 UniRef100_A7PMD8 vulgaris Chromosome chr14 scaffold_21,whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID =A7PMD8_VITVI 7.00E−91 TC260900 GMGI.071508 1065796 1069134 weaklysimilar to UniRef100_A7PMD8 Cluster: Chromosome chr14 scaffold_21 =whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosomechr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera(Grape) = partial (41%) TA63020_3847 Glycine_(—) 1067436 1069134 NAmax_release_(—) 2 CA783703 Glycine_(—) 1068257 1068879 NAsoja_release_(—) 2 TA58065_3847 Glycine_(—) 1074998 1076541AT3g28050/MMG15_6 max_release_(—) [Arabidopsis thaliana 2 (Mouse-earcress)] TC251785 GMGI.071508 1074998 1076541 similar to UniRef100_Q8L9I2Cluster: Nodulin MtN21- like protein; n = 1; Arabidopsis thaliana|Rep:Nodulin MtN21-like protein - Arabidopsis thaliana (Mouse-ear cress) =partial (16%) CB280623 Phaseolus_(—) 1075036 1076540 AT3g28050/MMG15_6vulgaris_(—) [Arabidopsis thaliana release_2 (Mouse-ear cress)] EH043320Arachis_(—) 1075056 1077422 Cluster: Hypothetical stenosperma_(—)protein, n = 1, Medicago release_5 truncatula|Rep: Hypotheticalprotein - Medicago truncatula (Barrel medic) asmbl_11886 Vigna_(—)1075036 1077585 NA unguiculata BQ094260 Glycine_(—) 1075548 1077551Nodulin-like protein max_release_(—) [Arabidopsis thaliana 2 (Mouse-earcress)] BF598290 Glycine_(—) 1075557 1077593 Nodulin-like proteinsoja_release_(—) [Arabidopsis thaliana 2 (Mouse-ear cress)] Pvcon6314Phaseolus_(—) 1075036 1078733 UniRef100_A7PMD8 vulgaris Chromosome chr14scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis viniferaRepID = A7PMD8_VITVI 1.00E−105 TA58064_3847 Glycine_(—) 1075337 1079189AT3g28050/MMG15_6 max_release_(—) [Arabidopsis thaliana 2 (Mouse-earcress)] TC255833 GMGI.071508 1075337 1079189 weakly similar toUniRef100_A7PMD8 Cluster: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) =partial (64%) BG042956 Glycine_(—) 1078885 1079014 NA soja_release_(—) 2TC263589 GMGI.071508 1086875 1091139 similar to UniRef100_A7PME0Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n= 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genomeshotgun sequence - Vitis vinifera (Grape) = partial (35%) TA50577_3847Glycine_(—) 1086875 1094082 Alpha-dioxygenase [Pisum max_release_(—)sativum (Garden pea)] 2 asmbl_11887 Vigna_(—) 1089135 1092345 NAunguiculata CA410123 Lupinus_(—) 1092182 1092694 Alpha-dioxygenase[Pisum albus_release_(—) sativum (Garden pea) 2 Pvcon4974 Phaseolus_(—)1091225 1093836 UniRef100_Q5GQ66 vulgaris Alpha-dioxygenase n = 1 Tax =Pisum sativum RepID = Q5GQ66_PEA E-0 TC243973 GMGI.071508 10911771094141 similar to UniRef100_Q5GQ66 Cluster: Alpha- dioxygenase; n = 1;Pisum sativum|Rep: Alpha- dioxygenase - Pisum sativum (Garden pea) =partial (61%) asmbl_11888 Vigna_(—) 1092518 1093829 NA unguiculataM0206286 SEQ. 1209562 1210392 SEQ ID NO: 17 Listing M0206054 SEQ.1465522 1465187 SEQ ID NO: 18 Listing M0205375 SEQ. 2010060 2009541 SEQID NO: 19 Listing toGm13 DAGchainer 1046081 4647877 Ks0.2059 NA Glyma1 150600000 NA

Sequences for the genes provided above can be obtained from the WorldWide Web (or Internet) using the identifiers provided in Column 1(Locus/Display Name) or Column 5 (ADDITIONAL LOCUS INFORMATION) from thefollowing internet locations: “soybase.org” (described in Grant et al.,Nucleic Acids Research, 2010, Vol. 38, Database issue D843-D846) orsoybase.org/gbrowse/cgi-bin/gbrowse/gmax1.01/ (see Hyten D L, Choi I-Y,Song Q, Specht J E, Carter T E et al. (2010) A high density integratedgenetic linkage map of soybean and the development of a 1,536 UniversalSoy Linkage Panel for QTL mapping. Crop Science 50:960-968. (CropScience); and Hyten D L, Cannon S B, Song Q, Weeks N, Fickus E W et al.(2010) High-throughput SNP discovery through deep resequencing of areduced representation library to anchor and orient scaffolds in thesoybean whole genome sequence. BMC Genomics 11(1): 38);

“phytozome.net” or “phytozome.net/cgi-bin/gbrowse/soybean/ ?name=Gm09”;“www.plantgdb.org” or “plantgdb.org/GmGDB/(Assembly version Glyrnal.170(Apr 2009)” ; and, “ncbi.nlm.nih.gov/sites/entrez” and subsites“ncbi.nlm.nih.gov/nucest”, “ncbi.nlm.nih.gov/dbEST”,“ncbi.nlm.nih.gov/genbank/”, “.ncbi.nlm.nih.gov/sites/genome”,“ncbi.nlm.nih.gov/unigene”, and “ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=3847”.

We claim:
 1. A method of identifying a soybean plant that comprises agenotype associated with dicamba tolerance and reproductive tolerance toglyphosate, comprising: detecting in a soybean plant an allele in atleast one genetic locus associated with dicamba tolerance andreproductive tolerance to glyphosate, wherein the genetic locus is in alinkage group L genomic region flanked by loci M0205928 (SEQ ID NO: 4)and BU765955 (SEQ ID NO: 12), and denoting that said plant comprises agenotype associated with dicamba tolerance.
 2. The method of claim 1,wherein said method further comprises the step of selecting said denotedplant from a population of plants.
 3. The method of claim 1, whereinsaid plant comprises a transgene that confers resistance to dicambaand/or a transgene that confers resistance to glyphosate.
 4. The methodof claim 3, wherein said soybean plant or progeny thereof is exposed toa dosage of dicamba sufficient to cause a deleterious effect in asusceptible variety comprising the transgene and/or is exposed to adosage of glyphosate sufficient to cause sterility in a susceptiblevariety comprising the transgene(s).
 5. The method of claim 2, wherein aplant that exhibits dicamba tolerance and/or reproductive tolerance toglyphosate is selected.
 6. The method of claim 1, wherein said genotypeassociated with a dicamba tolerance comprises at least one polymorphicallele of at least one marker in a first sub-region of said linkagegroup L region that is flanked by loci M0205928 (SEQ ID NO: 4) andM0129138 (SEQ ID NO: 6) and/or at least one polymorphic allele of atleast one marker in a second sub-region of said linkage group L regionthat is flanked by loci BU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO:12) and/or at least one polymorphic allele of at least one marker in athird sub-region of said linkage group L region that is flanked by lociBU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8).
 7. The method of claim1, wherein said genotype associated with dicamba tolerance comprises atleast one polymorphic allele of at least one marker in said linkagegroup L region selected from the group consisting of a TT alleleM0205350 (SEQ ID NO: 10), a TT allele of M0101742 (SEQ ID NO: 5), a CCallele of M0102027 (SEQ ID NO: 11), and an AA allele of NGMAX008197032(SEQ ID NO:52).
 8. A method for obtaining a soybean plant comprising inits genome at least one dicamba tolerance locus, compromising the stepsof: (a) genotyping a plurality of soybean plants with respect to atleast one genetic locus in a linkage group L genomic region flanked byloci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12); and (b)selecting a soybean plant comprising in its genome at least one geneticlocus comprising a genotype associated with dicamba tolerance.
 9. Themethod of claim 8, wherein said genotype associated with dicambatolerance comprises at least one polymorphic allele of at least onemarker in a first sub-region of said linkage group L region flanked byloci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at leastone polymorphic allele of at least one marker in a second sub-region ofsaid linkage group L region that is flanked by loci BU551363 (SEQ ID NO:9) and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic alleleof at least one marker in a third sub-region of said linkage group Lregion that is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQID NO:8).
 10. The method of claim 8, wherein said genotype associatedwith dicamba tolerance comprises at least one polymorphic allele of atleast one marker in said first linkage group L region, said firstsub-region, or said second sub-region, wherein said marker is selectedfrom the group consisting of a TT allele M0205350 (SEQ ID NO: 10), a TTallele of M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO:11), and an AA allele of NGMAX008197032 (SEQ ID NO:52).
 11. The methodof claim 8, wherein said plurality of soybean plants comprises apopulation that is obtained by: i) crossing a parent plant comprising atleast one dicamba tolerance locus with a parent plant comprising atleast one dicamba sensitivity locus; or, ii) obtaining seed or progenyfrom a parental plant segregating for at least one dicamba tolerancelocus.
 12. The method of claim 8, wherein said population containsplants that comprise a transgene that confers resistance to dicambaand/or a transgene that confers resistance to glyphosate.
 13. The methodof claim 8, further comprising the step of assaying for the presence ofat least one additional marker, wherein said additional marker is eitherlinked or unlinked to said linkage group L genomic region.
 14. Themethod of claim 8, wherein said plurality of soybean plants, saidsoybean plant, and/or progeny thereof are exposed to a dosage of dicambasufficient to cause a deleterious effect in a susceptible varietycomprising the transgene and/or is exposed to a dosage of glyphosatesufficient to cause sterility in a susceptible variety comprising thetransgene.
 15. The method of claim 8, wherein a plant that exhibitsdicamba tolerance and/or reproductive tolerance to glyphosate isselected.
 16. A method for producing a soybean plant comprising in itsgenome at least one introgressed dicamba tolerance locus comprising thesteps of: (a) crossing a first soybean plant with a dicamba tolerancelocus with a second soybean plant comprising: a dicamba sensitivitylocus in a first linkage group L genomic region flanked by loci M0205928(SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6) and/or at least onepolymorphic allele of at least one marker in a second sub-region of saidlinkage group L region that is flanked by loci BU551363 (SEQ ID NO: 9)and BU765955 (SEQ ID NO: 12) and/or at least one polymorphic allele ofat least one marker in a third sub-region of said linkage group L regionthat is flanked by loci BU55345 (SEQ ID NO:7) and M0114388 (SEQ ID NO:8)and at least one linked polymorphic locus not present in said firstsoybean plant to obtain a population segregating for the dicambatolerance loci and said linked polymorphic locus; (b) detecting at leasttwo polymorphic nucleic acids in at least one soybean plant from saidpopulation, wherein at least one of said polymorphic nucleic acids islocated in said first linkage group L region and/or said second linkagegroup L region and wherein at least one of said polymorphic amino acidsis a linked polymorphic locus not present in said first soybean plant;and (c) selecting a soybean plant comprising a genotype associated withdicamba tolerance and at least one linked marker found in said secondsoybean plant comprising a dicamba sensitivity locus but not in saidfirst soybean plant, thereby obtaining a soybean plant comprising in itsgenome at least one introgressed dicamba tolerance locus.
 17. The methodof claim 16, wherein at least one of said first or said second soybeanplants comprises a transgene that confers resistance to dicamba and/or atransgene that confers resistance to glyphosate.
 18. The method of claim17, wherein said population, said selected soybean plant, and/or progenyof selected soybean plant is exposed to a dosage of dicamba sufficientto cause a deleterious effect in a susceptible variety comprising thetransgene and/or is exposed to a dosage of glyphosate sufficient tocause sterility in a susceptible variety comprising the transgene. 19.The method of claim 16, wherein said polymorphic nucleic acid detectedin step (b) is detected with at least one marker selected from the groupconsisting of M0205350 (SEQ ID NO: 10), M0101742 (SEQ ID NO: 5),M0102027 (SEQ ID NO: 11), and NGMAX008197032 (SEQ ID NO:52).
 20. Themethod of claim 16, wherein said polymorphic nucleic acid detected instep (b) comprises a TT allele of M0205350 (SEQ ID NO: 10), a TT alleleof M0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), andan AA allele of NGMAX008197032 (SEQ ID NO:52).
 21. The method of claim20, wherein said polymorphic nucleic acid detected in step (b) isdetected with marker M0205350 (SEQ ID NO: 10), M0102027 (SEQ ID NO: 11),or marker NGMAX008197032 (SEQ ID NO:52).
 22. The method of claim 20,wherein said polymorphic nucleic acids are detected with marker M0101742(SEQ ID NO: 5).
 23. The method of claim 16, wherein said linkedpolymorphic locus is detected with a genotypic marker, a phenotypicmarker, or both.
 24. The method of claim 23, wherein said linkedpolymorphic locus is detected with a marker that is located within about1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of said dicambatolerance locus.
 25. The method of claim 24, wherein said linkedpolymorphic locus is detected with at least one marker selected from thegroup consisting of asmbl_(—)11856 (SEQ ID NO: 1), TC122822 (SEQ ID NO:2), BI967232 (SEQ ID NO: 3), M0205537 (SEQ ID NO: 15), M0202715 (SEQ IDNO: 16), M0206286 (SEQ ID NO: 17), M0206054 (SEQ ID NO:18), and M0205375(SEQ ID NO: 19).
 26. A transgenic soybean plant comprising introgressedlinkage group L regions comprising at least one polymorphic allele of atleast one marker in a first sub-region of said linkage group L regionthat flanked by loci M0205928 (SEQ ID NO: 4) and M0129138 (SEQ ID NO: 6)and/or at least one polymorphic allele of at least one marker in asecond sub-region of said linkage group L region that is flanked by lociBU551363 (SEQ ID NO: 9) and BU765955 (SEQ ID NO: 12) and/or at least onepolymorphic allele of at least one marker in a third sub-region of saidlinkage group L region that is flanked by loci BU55345 (SEQ ID NO:7) andM0114388 (SEQ ID NO:8), wherein said polymorphic alleles are associatedwith dicamba tolerance and/or reproductive tolerance to glyphosate, andwherein said plant comprises a transgene that confers resistance todicamba.
 27. The transgenic plant of claim 26, wherein said polymorphicalleles comprise a TT allele of M0205350 (SEQ ID NO: 10), a TT allele ofM0101742 (SEQ ID NO: 5), a CC allele of M0102027 (SEQ ID NO: 11), and anAA allele of NGMAX008197032 (SEQ ID NO:52).
 28. The transgenic plant ofclaim 26, wherein said plant exhibits dicamba tolerance.
 29. Thetransgenic plant of claim 26, wherein said plant further comprises atransgene that confers resistance to glyphosate and exhibitsreproductive tolerance to glyphosate.
 30. The transgenic plant of claim26, wherein said plant further comprises at least one transgeneconferring resistance to a herbicide selected from the group consistingof a 2,4-D, glufosinate, bromoxynil, synthetic auxins other than 2,4-D,acetolactate synthase (ALS), acetyl CoA carboxylase (ACCase),hydroxyphenyl pyruvate dioxygenase (HPPD), and a sulfonylurea herbicideand/or at least one transgene selected from the group of transgenesconferring insect resistance, nematode resistance, fungal resistance, animprovement in seed oil quantity, an improvement in seed oil quality,abiotic stress resistance, and intrinsic yield increases.
 31. A methodof identifying a transgenic soybean plant that comprises a genotypeassociated with reproductive tolerance to glyphosate, the methodcomprising: (a) scoring at least one transgenic plant in a population oftransgenic soybean plants that had been exposed to dicamba for dicambatolerance, said plants having a transgene that confers resistance todicamba; and, (b) selecting a transgenic plant that exhibits dicambatolerance, thereby identifying a transgenic soybean plant that comprisesa genotype associated with reproductive tolerance to glyphosate.
 32. Themethod of claim 31, wherein said population is segregating for to atleast one genetic locus in a linkage group L genomic region flanked byloci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12) that isassociated with dicamba tolerance.
 33. The method of claim 31, whereinsaid method further comprises genotyping the selected soybean plant withrespect to at least one genetic locus in a linkage group L genomicregion flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO:12).
 34. The method of claim 31, wherein said selected transgenic plantfurther comprises a transgene that confers resistance to glyphosate andwherein said selected transgenic plant or progeny thereof is scored forreproductive tolerance to glyphosate following exposure to glyphosate.35. The method of claim 31, further comprising exposing said populationof transgenic soybean plants to dicamba.
 36. The method of claim 31,wherein dicamba tolerance is scored by determining a reduction inmalformation when compared to a dicamba sensitive transgenic plant thatcomprises said transgene that confers resistance to dicamba.
 37. Amethod of identifying a transgenic soybean plant that comprises agenotype associated with tolerance to dicamba, comprising: (a) scoringat least one plant in a population of transgenic soybean plants that hadbeen exposed to glyphosate for reproductive tolerance to glyphosate,wherein said plants comprise a transgene that confers resistance toglyphosate; and, (b) selecting a transgenic plant that exhibitsreproductive tolerance to glyphosate, thereby identifying a transgenicsoybean plant that comprises a genotype associated with dicambatolerance.
 38. The method of claim 37, wherein said population issegregating for to at least one genetic locus in a linkage group Lgenomic region flanked by loci M0205928 (SEQ ID NO: 4) and BU765955 (SEQID NO: 12) that is associated with dicamba tolerance.
 39. The method ofclaim 37, wherein said method further comprises genotyping the selectedsoybean plant with respect to at least one genetic locus in a linkagegroup L genomic region flanked by loci M0205928 (SEQ ID NO: 4) andBU765955 (SEQ ID NO: 12).
 40. The method of claim 37, wherein saidselected transgenic plant further comprises a transgene that confersresistance to dicamba and wherein said selected transgenic plant orprogeny thereof is scored for tolerance to dicamba following exposure todicamba.
 41. The method of claim 37, further comprising exposing saidpopulation of transgenic soybean plants to glyphosate.
 42. The method ofclaim 37, wherein glyphosate reproductive tolerance is scored bydetermining a reduction in sterility when compared to a transgenic plantthat exhibits glyphosate reproductive sensitivity and comprises saidtransgene that confers resistance to glyphosate.
 43. A method ofobtaining a transgenic soybean plant that comprises a genotypeassociated with reproductive tolerance to glyphosate, the methodcomprising: (a) exposing a population of transgenic soybean plants todicamba, wherein said plants have a transgene that confers resistance todicamba; (b) observing dicamba tolerance exhibited by one or moresoybean plants following exposure to dicamba; and, (c) selecting atransgenic plant that exhibits dicamba tolerance, thereby obtaining atransgenic soybean plant that comprises a genotype associated withreproductive tolerance to glyphosate.
 44. The method of claim 43,wherein said population is segregating for to at least one genetic locusin a linkage group L genomic region flanked by loci M0205928 (SEQ ID NO:4) and BU765955 (SEQ ID NO: 12) that is associated with dicambatolerance.
 45. The method of claim 43, wherein said method furthercomprises genotyping the selected soybean plant with respect to at leastone genetic locus in a linkage group L genomic region flanked by lociM0205928 (SEQ ID NO: 4) and BU765955 (SEQ ID NO: 12).
 46. The method ofclaim 43, wherein said selected transgenic plant further comprises atransgene that confers resistance to glyphosate and wherein saidselected transgenic plant or progeny thereof is scored for reproductivetolerance to glyphosate following exposure to glyphosate.
 47. The methodof claim 43, wherein dicamba tolerance is scored by determining areduction in malformation when compared to a dicamba sensitivetransgenic plant that comprises said transgene that confers resistanceto dicamba.